@Phaedrux, @bricor, @jumpedwithbothfeet ... Gentlemen. What a feast of knowledge in this trail. Wow...Thank you all. Sometimes the forest does not let you see the tree....

Each one of you hold a piece of the puzzle...
@Phaedrux, thanks for Ockham’s razor application: The simplest solution is the right one. I re-wired using the 2 wire cable connected to the ends of the motherboard endstop connector.

@Bricor, inverting the polarity of the connection by software was brilliant. The RRF equivalent selection was x-stop inverse.

@jumpedwithbothfeet, Ender 5 end stops are normally closed!!!. You see the little metal lever open...but when you test it....the circuit is closed... Thanks for the config file. I don’t know how did you assign I04 and I05 to the end stops, so I am still far away form your level of illumination

Now, after all this, standing in front of the printer 0,0 is on the nearest left corner. The end stops are on the far right corner.
From the center of the bed:
Negative values of x move the head left
Negative values of Y move the head towards me
Positive values of Z move the bed downwards

I still have questions on the z-stop and BLTouch proper nomenclature.
Basics of Gcoding with the differences between S1 or S2.... But the printer works....so I will try to give you a free Sunday.

Thank you guys!

@Phaedrux
I have not posted in a while and I wanted to thank for all the help received, by posting the latest config for the machine.
Best configuration (so far) working with Simplify 3D. Please uncheck the boxes as per this picture to let the firmware control the printing.

The config is below
; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2.1.8 on Sun Apr 19 2020 17:01:43 GMT-0400 (Eastern Daylight Time)

; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Daniel Ender 5 Duet 2 Wifi" ; set printer name

; Network
M552 S1 ; enable network
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet

; Drives
M569 P0 S0 ; physical drive 0 goes backwards
M569 P1 S0 ; physical drive 1 goes backwards
M569 P2 S0 ; physical drive 2 goes backwards
M569 P3 S1 ; physical drive 3 goes forwards
M584 X0 Y1 Z2 E3 ; set drive mapping
M350 X16 Y16 Z16 E16 I1 ; configure microstepping with interpolation
M92 X80.00 Y80.00 Z811.00 E409.00 ; set steps per mm
M566 X900.00 Y900.00 Z60.00 E4000.00 ; set maximum instantaneous speed changes (mm/min)
M201 X6000.00 Y6000.00 Z60.00 E4000.00 ; set accelerations (mm/s^2)
M203 X15000.00 Y15000.00 Z600.00 E8000.00 ; set maximum speeds (mm/min)
M204 P800 T2000 ; set accel for XY print (P) and travel moves (T).
M207 S0.85 R-0.000 F3200 T2600 Z0.0 ; set firmware retraction
M572 D0 S0.050 ; set pressure advance
M906 X850 Y850 Z850 E850 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X220 Y220 Z300 S0 ; set axis maxima

; Endstops
M574 X2 S1 P"xstop" ; configure active-high endstop for high end on X via pin xstop
M574 Y2 S1 P"ystop" ; configure active-high endstop for high end on Y via pin ystop
M574 Z1 S2 ; configure Z-probe endstop for low end on Z

; Z-Probe
M950 S0 C"exp.heater3" ; create servo pin 0 for BLTouch
M558 P9 C"zprobe.in" H5 F120 T12000 ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X-45 Y3 Z1.95 ; set Z probe trigger value, offset and trigger height
M557 X15:160 Y15:200 S20 ; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T98801 B4185 ; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0 ; create bed heater output on bedheat and map it to sensor 0
M143 H0 S120 ; set temperature limit for heater 0 to 120C
M307 H0 A88.4 C265.5 D2.0 S1.00 V23.9 B0 ; disable bang-bang mode for the bed heater and set PWM limit (Values copied from auto tune D corrected from 0.9 to 2 by Phaedrux)
M140 H0 ; map heated bed to heater 0
M308 S1 P"e0temp" Y"thermistor" T98801 B4185 ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1 ; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S300 ; set temperature limit for heater 1 to 300C
M307 H1 A390.6 C153.8 D3.5 S1.00 V23.9 B0 ; disable bang-bang mode for heater and set PWM limit (Values copied from auto tune)

; Fans
M950 F0 C"fan0" Q500 ; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1 ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"fan1" Q500 ; create fan 1 on pin fan1 and set its frequency
M106 P1 S1 H1 T45 ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 S"E3D V6 Nozzle X" D0 H1 F0 ; define tool 0
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined

; Miscellaneous
M911 S10 R11 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; set voltage thresholds and actions to run on power loss

Enjoy printing!!!

@Phaedrux said in Orbiter 2.0 + filament sensor:

M98 P"config.g"

Phaedrux,
This is the message I get from the console
M98 P"config.g"
WiFi module is connected to access point Daniel at Home 5.0, IP address 192.168.1.40
FTP is enabled on port 21
TELNET is enabled on port 23
Error: Heater 1 not switched on due to bad model
Warning: Heater 0 predicted maximum temperature at full power is 260°C
Warning: Heater 0 predicted maximum temperature at full power is 260°C

@Daniel
My config is

; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.1.4 on Tue Oct 13 2020 12:04:59 GMT-0400 (Eastern Daylight Time)

; Duet G-code:               https://duet3d.dozuki.com/Wiki/Gcode
; RRF3 G-code meta commands: https://duet3d.dozuki.com/Wiki/GCode_Meta_Commands
; RRF3 Object model:         https://duet3d.dozuki.com/Wiki/Object_Model_of_RepRapFirmware
; RRF3 Pin Names:            https://duet3d.dozuki.com/Wiki/RepRapFirmware_3_overview#Section_Pin_names_for_Duet_2_WiFi_Ethernet

; #### Debugging
M111 S0                     ; Debug off
M929 P"eventlog.txt" S1     ; Start logging to file eventlog.txt
M550 P"Daniel's RailCore"   ; Machine name and Netbios name (can be anything you like)

;M540 P2c:3a:e8:0b:09:f7    ; Set MAC address (unused on DuetWifi)
M552 S1                     ; Enable networking
M552 P0.0.0.0               ; Use DHCP

; #### General preferences
M555 P0                     ; Set output to look like RepRap_Firmware
M575 P1 B57600 S1           ; Comms parameters for PanelDue
G21                         ; Work in millimetres
G90                         ; Send absolute coordinates...
M83                         ; ...but relative extruder moves

; #### Networking and Communications
M552 S1                     ; Enable WiFi
M586 P1 S1                  ; Enable FTP
;M551 P"myrap"              ; Machine password (used for FTP), leave disabled for anonymous login on a local network.
M586 P2 S1                  ; Enable Telnet

; #### Axis and motor configuration
M669 K1                     ; CoreXY mode
M350 X16 Y16 Z16 E16:16     ; Set 16x microstepping for axes & extruder, with interpolation.
M92 X200 Y200               ; Set 200 steps/mm for XY (0.9 deg/step . 16 tooth pulley and GT2 belt)
;M92 X100 Y100              ; Set 100 steps/mm for XY (1.8 deg/step . 16 tooth pulley and GT2 belt) CHEAPCORE SPECIFIC

; #### Drives
M584 X0 Y1 Z5:6:7 E3:4:8:9  ; Map Z to drivers 5, 6, 7. Define unused drivers 3,4,8 and 9 as extruders
M569 P0 S0                  ; Drive 0 goes forwards (change to S0 to reverse it)| X stepper
M569 P1 S1                  ; Drive 1 goes backwards(change to S1 to reverse it)| Y Stepper
M569 P2 S1                  ; Drive 2 goes forwards                             | Unused
M569 P3 S0                  ; Drive 3 goes backwards                            | Extruder S0 for Bondtech, S0 for Titan
M569 P4 S1                  ; Drive 4 goes forwards                             | Extruder (unused)
M569 P5 S0                  ; Drive 5 goes backwards                            | Front Left Z
M569 P6 S0                  ; Drive 6 goes backwards                            | Rear Left Z
M569 P7 S0                  ; Drive 7 goes backwards                            | Right Z

; #### Leadscrew locations
;Front left,(-13,22) Rear Left (-12,277) , Right (343,151) S7.5 is the max correction - measure your own offsets, to the bolt for the yoke of each leadscrew
M671 X-13:-13:343  Y22:277:151 S7.5  

; #### Endstop Configuration - sensorless
;M574 X1 S3                                ; _RRF3_ set X endstop to xstop port sensorless
;M574 Y1 S3                                ; _RRF3_ set Y endstop to ystop port sensorless
;M915 P0:1 S3 R0 F0                        ; Both motors because corexy; Sensitivity 3, don’t take action, don’t filter

; #### Endstop Configuration - microswitches
M574 X1 S1 P"xstop"                      ; _RRF3_ set X endstop to xstop port (switch/active high)
M574 Y1 S1 P"ystop"                      ; _RRF3_ set Y endstop to ystop port (switch/active high)

; #### Current, speeds and Z/E step settings
; ##########################################
; Conservative speeds for commissioning
;M906 X1150 Y1150 Z900 E560 I60   ; Motor currents (mA) - WARNING: Conservative - May trigger stallguard (and prematurely during homing) if sensorless.
;M201 X1000 Y1000 Z30 E500        ; Accelerations (mm/s^2) - WARNING: Conservative
;M203 X3000 Y3000 Z50 E1800       ; Maximum speeds (mm/min) - WARNING: Conservative
;M566 X300 Y300 Z30 E500          ; Maximum jerk speeds mm/minute - WARNING: Conservative

; Fully commissioned speeds.
M906 X2100 Y2100 Z1000 E1200 I25  ; Set motor currents (mA) and idle at 25%
M201 X3000 Y3000 Z100 E3000       ; Accelerations (mm/s^2)
M203 X24000 Y24000 Z600 E7200     ; Maximum speeds (mm/min)
M566 X1000 Y1000 Z100 E600        ; Maximum jerk speeds mm/minute

M92 Z1600                         ; Leadscrew motor axis steps/mm for Z - TR8*2 / 1.8 deg stepper or TR8*4 / 0.9 deg stepper
;M92 E837                         ; Extruder steps/mm - 1.8 deg/step Steps/mm (Standard BMG pancake stepper 17HS10-0704S)
;M92 E400                         ; Extruder Bondtech LGX  
;M92 E421.05 					  ; Extruder Bondtech LGX Corrected with Atomic PETG CF@235 Nozzle X0.4
M92 E690                          ; LDO Orbiter Extruder steps/mm - 1.8 deg/step Steps/mm Nozzle X0.6


; Set travel acceleration
M558 T18000 F500                  ; Set Z probe Travel speed

; Kit settings - uncomment for kit
; M92 Z1600                        ; Steps/mm for Z - TR8*2 / 1.8 deg stepper or TR8*4 / 0.9 deg stepper
; M92 E837                         ; Extruder - 0.9 deg/step (ProjectR3D kit with E3D stepper MT-1701HSM140AE or Standard Titan stepper 42BYGHM208P4.5-15-X2)




; ####  Set axis minima:maxima switch positions
; Adjust to suit your machine and to make X=0 and Y=0 the edges of the bed
;M208 X0:250 Y0:250 Z-0.2:230      ; Conservative 300ZL/T settings (or 250ZL) ; These values are conservative to start with, adjust during commissioning.
M208 X0:305 Y0:300 Z0:320          ; 300ZL

; #### Fan definitions; #####################

M950 F0 C"fan0"                                          ; Set Fan 0 on "Duet2 Fan 0" for Part Cooling fan
M950 F1 C"fan1" Q25000                                   ; Set Fan 1 on "Duex2 Fan 1" for Hotend Fan. Use the FAN1 connector for a thermostatically-controlled 
                                                         ; hot end fan, because on the Duet 2 it defaults to being on at power up, to provide maximum safety 
                                                         ; if you restart your Duet when the hot end is hot.
M106 P0 S0 H-1                                           ; (Part cooling fan) Set fan 0 value, Thermostatic control is OFF
M106 P1 C"Mosquito" H1 T40 S0.7                            ; Set fan 1. Thermostatic control is ON for Heater 1 (Hotend fan) S0.7=75% speed


; #### Tool definitions; #####################
; #### Tool E0 / Heater 1 - Slice engineering

M950 H1 C"e0heat" T1                                                              ; Heater 1 is Hotend heater is on e0heat
M308 S1 P"spi.cs1" Y"rtd-max31865" A"e0_heat" T"k" F60 							  ; create sensor number 1 as a PT100 sensor in the first position on the Duet 2 daughter board connector
;M308 S1 P"e0temp" Y"thermistor" A"e0_heat" T100000 B4725 R4700 C7.06e-8 H0 L0    ; E0 thermistor,
M563 P0 S"Mosquito" D0 H1 F0                                                      ; Define tool 0 uses extruder 0, heater 1 ,Fan 0

G10 P0 X0 Y0 Z0 S-273.1 R-273.1                                                   ; Set tool 0 axis offsets and operating and standby temperatures
M143 H1 S320                                                                      ; Maximum Extruder 0 temperature (E3D requires 285C to change nozzle)
M570 H1 P5 T15                                                                    ; Configure heater fault detection
                                                                                  ; Hnnn Heater number
                                                                                  ; Pnnn Time in seconds for which a temperature anomaly must persist
                                                                                  ; on this heater before raising a heater fault.
                                                                                  ; Tnnn Permitted temperature excursion from the setpoint for this heater (default 15C);

; #### Filament options
; #####################
M200 D1.75                                           ; Set filament diameter for future volumetric extrusion.
; Volumetric extrusion is an option you can set in some slicers whereby all extrusion amounts are specified in mm3 (cubic millimetres) of filament instead of mm of filament. 
; This makes the gcode independent of the filament diameter, potentially allowing the same gcode to run on different printers.

; #### Filament runout for E0
M950 J1 C"^connlcd.encb"								; Define logical input for filament autoload for Orbiter 2.0
M581 P1 T2 S0 R0									; Define trigger for filament autoload triggers trigger2.g for Orbiter 2.0
M950 J2 C"^connlcd.enca"								; Define logical input for filament unload for Orbiter 2.0
M581 P2 T3 S0 R0 									; Define trigger for filament autoload triggers trigger3.g for Orbiter 2.0

; M591 D0 P1 C"e0_stop" S1                 		    ; Enable Sentinel Dyze filament sensor runout (disabled)
; M591 D0 P5 C"e0stop" R30:130 E3.0 S0				; Enable Duet laser filament monitor sensor
; Configure filament sensing
; D0 - Extruder 0
; P - Sensor type - 1=simple sensor (high signal when filament present), 5= Duet Laser v2.0, 6= Duet Laser v2.0 with microswitch
; C - Which input the filament sensor is connected to. On Duet electronics: 3=E0 endstop input
; S = 0 to disable comparison of commanded vs. measured output, 1 to enable comparison and pause the print if a discrepancy is detected

; #### Z probe
; ############
; #### Z probe and compensation definition

; *** If you have a switch instead of an IR probe, change P1 to P4 in the following M558 command
; IR Probe - uncomment the following 2 lines if you have a and IR Probe, and comment out the BLTouch section below
; #####################
; M558 P1 C"^zprobe.in"
; G31 X0 Y35 P500                             ; Probe offset and "stop" value.
; M558 F750                                   ; Z probe - raise probe height.
                                              ; H10 - dive height
                                              ; A bigger dive height prevents a situation where the bed is out of alignment by more than the dive
                                              ; height on any corner, which can crash the hot-end into the bed while moving the head in XY.
                                              ; Probing speed and travel speed are similarly reduced in case the Z probe is not connected properly
                                              ; (or disconnects later after moving to a point) giving the user more time to stop.

; BLTouch - comment out the following 3 lines if using a IR Probe
; #####################
; M558 P9 C"^zprobe.in" F100 H5 R0.2 T6000 A5 S0.02         ; _RRF3_ BLTouch connected to Z probe IN pin
; M950 S0 C"duex.pwm1"				   ; _RRF3_ Define BLTouch Servo (S0) on duet pwm1

; G31 X-3.5 Y36 Z2.927 S0.02		   	; Customize your offsets appropriately - do a paper test, and put the probed value in the Z value here
; G31 X-7.13 Y23.39 Z2.026 S0.02		   	; Setting for the Bondetch LGX + Mosquito magnum (note: Z positive number is closer to the bed)

; #### General probing configuration and offsets 
; G31 Z2.026 S0.02                     ; M558 settings for all probes

; Euclid Probe Settings RRF 3.x on Duet2
; #####################
; Endstop type S0 (active low switch) is no longer supported in M574 commands. 
; Instead, use type S1 and invert the input by prefixing the pin name with '!'.
; example to have multiple endstops on leadscrews
; M574 Z1 S1 P"zstop+e1stop" ; configure active-high endstops for low end on Z via pins zstop and e1stop
; Make sure that the two endstops are defined in the same order in the M574 command 
; as the corresponding Z motors in your M584 command. 

M574 Z1 S2                                    ; configure Z-probe endstop for low end on Z
M558 K0 P5 C"^zprobe.in" H8 F300 60 T9000 A3 S0.01      
                                              ; K0 for probe 0, P5 for NC switch, C for input pin, 
                                              ; ^ for enabling the native pullup resistor on Duet 2 
                                              ; hardware running RRF3  
                                              ; H dive height of 8mm, F300 probing speed 6mm/sec, 
                                              ; T9000 travel speed 150mm/sec,   
                                              ; A3 number of probes 1, S0.01 max tolerance of 0.01 
G31 K0 P500 X4.66 Y28.9 Z6.459                ; CHECK for LOOSE things first! set Z probe trigger 
                                              ; value, offset and trigger height.  Higher numbers
                                              ; makes nozzle closer to bed
                                              ; switch plunger is 16.4mm to the LEFT and 29.27mm in
                                              ; FRONT of the nozzle. Switch triggers 0.9mm BELOW nozzle
                                              ; https://duet3d.dozuki.com/Wiki/Test_and_calibrate_the_Z_probe#Section_Fine_tuning_the_trigger_height
                                              ; if you have to move the nozzle away from the bed, 
                                              ; decrease the G31 Z value by the amount of baby stepping used


; ##### Mesh
; M557 X20:280 Y20:280 S20 S20                ; Set Default Mesh (conservative)
; M557 X10:290 Y45:255 S20:30                 ; Set Mesh for probe
; M557 X93.37:218.37 Y85.39:195.39 P2:2       ; 4 points for bed leveling avoiding magnets
M557 X15:290 Y40:263 P2 		    		  ; Mesh for Euclid leveling
M376 H5

; #### Bed - Heater 0
M950 H0 C"bedheat" T0                         ;_RRF3_ define Bed heater is on bedheat **
M308 S0 P"bedtemp" Y"thermistor" A"bed_heat" T100000 B3950 R4700 H0 L0  ;_RRF3_ Bed thermistor, connected to bedtemp on Duet2
; M308 S8 P"exp.thermistor7" Y"thermistor" A"keenovo" T100000 B3950 R4700  H0 L0  ; Silicone heater thermistor on x7
M570 S360                                     ; Print will be terminated if a heater fault is not reset within 360 minutes.
M140 H0                                       ; (H0 as per 3.0 RC11 ** before M143 )
M143 H0 S120                                  ; Maximum bed temperature, if using a magbed this is important!

; #### Chamber - Heater 3 - (not enabled yet)
;M141 H3
;M950 H3 C"exp.heater3" T3                                                          ; heater 3 is the chamber heater
;M308 S3 P"exp.thermistor3" Y"thermistor" A"chamber high" T100000 B3950 R4700  H0 L0 ; Set Sensor 3 as 100K thermistor with B=3950 and a 4.7K series resistor
;M308 S4 P"exp.thermistor4" Y"thermistor" A"chamber low" T100000 B3950 R4700  H0 L0  ; Set Sensor 4 as 100K thermistor with B=3950 and a 4.7K series resistor
;M301 H3 B1                                                                         ; use bang-bang control for the chamber heater
;M106 P3 S1 H1 T50:80 C"Chamber"

; #### Electronics Cabinet
;M950 F7 C"duex.fan7"             ; Fan 7 on "Duex5 fan port 7"
;M950 F8 C"duex.fan8"             ; Fan 8 on "Duex5 fan port 8"

;M308 S10 Y"mcu-temp" A"mcu-temp" ; Set MCU on Sensor 10
;M106 P7 T35:55 H10 C"Elec.Cab.1" ; Electronics cooling fan that starts to turn on when the MCU temperature (virtual heater 100) reaches 45C
;M106 P8 T35:55 H10 C"Elec.Cab.2" ; and reaches full speed when the MCU temperature reaches 55C or if any TMC2660 drivers
                                 ; (N.B. If a fan is configured to trigger on a virtual heater whose sensor represents TMC2660 driver over-temperature
                                 ; flags, then when the fan turns on it will delay the reporting of an over-temperature warning for the corresponding drivers
                                 ; for a few seconds, to give the fan time to cool the driver down.)

; #### Compensation
M579 X1.0000 Y1.0000 Z1.0000              ; Scale Cartesian axes
;M556 S80 X0.8 Y0.3 Z0.72                 ; Axis compensation (measured with Orthangonal Axis Compensation piece)
M572 D0 S0.02                             ; Default Pressure Advance compensation
M207 S1.5 F7200 Z0.2					  ; Firmware retraction for Orbiter Extruder

; #### Default heater model (Overridden byconfig-override.g, but here in case config-override.g fails)
;M307 H0 A270.7 C90.4 D6.7 B0 S1.0          			; 700W Bed Heater settings.
;M307 H0 A251.2 C699.1 D11.9 S1.00 V24.2 B0 			; 300W Bed Heater settings.
M307 H0 B0 R0.243 C968.5 D33.11 S1.00 V24.1 			; Mag Bed mandala Roseworks with keenovo
;M307 H1 A666.7 C272.0 D3.6 S1.00 V24.1 B0  			; E3D Gold hotend settings.
;M307 H1 R2.842 C159.5 D3.30 S1.00 V24.1				; Mosquito mangum settings with 50W Slice Enginnering heather black 
;M307 H1 B0 R1.977 C178.3 D5.59 S1.00 V24.1				; Mosquito magnum with 40W E3D heater green
M307 H1 R2.176 K0.417:0.000 D4.28 E1.35 S1.00 B0 V24.1 	; Mosquito magnum, orbiter 2.0 with 40W E3D heater green 
M501                              ; Load saved parameters from non-volatile memory

; #### FINISH STARTUP.
; #### Custom area

; Ensure all temperatures are off and cleared.
M140 S0 R0               ; clear temperatures from DWC
M140 S-273.1 R0 	     ; Standby and initial Temp for bed as "off" (-273 = "off")
G10 P0 S-273.1 R-273.1   ; Set tool 0 operating and standby temperatures(-273 = "off")


G91                               ; Send relative coordinates.
G1 Z0.001 F99999 H2               ; Engage motors to prevent bed from moving after power on.
G90                               ; Send absolute coordinates.
T0								  ; Select tool 0.

The 2 lines of code for loading are as follows
M950 J1 C"^connlcd.encb"; define logical input for filament auto load
M581 P1 T2 S0 R0 ;define trigger for filament auto load triggers trigger2.g

The trigger2.g macro is
;Autoload filament macro
T0 ; select tool 0
M300 S2000 P100 ; play beep sound
M291 P"Filament autoloading!" S0 T3 ; display message
M302 P1 ; enable cold extrusion
G4 S1 ; wait for one second
G1 E15 F500 ; load filament inside the gears
M109 S235 T0 ; set hotend temperature and wait
G1 E200 F500 ; extrude 200mm, you may need to reduce speed for very soft TPU
M104 S0 T0 ; set hotend temperature to 0
M302 P0 ; disable cold extrusion
M291 P"Filament autoload complete!" S0 T3 ; display message

The unload lines of code in the config are:
M950 J2 C"^connlcd.enca"; define logical input for filament unload
M581 P2 T3 S0 R0 ; define trigger for filament auto load triggers trigger3.g

The trigger3.g macro is

;Auto unload filament macro
T0 ; select tool 0
M300 S4000 P100 ; play beep sound
M291 P"Filament unloading!" S0 T3 ; display message
M109 S235 T0 ; set hotend temperature to 235 and wait
G0 E-5 F3600 ; extract filament to cold end
G4 S3 ; wait for 3 seconds
G0 E5 F3600 ; push back the filament to strive stringing
G0 E-15 F3600 ; Extract fast in the cold zone
G0 E-70 F300 ; continue extraction slow allow filament to be cooled enough before reaches the gears
M104 S0 T0 ; set hotend temperature to 0
M291 P"Filament unload complete!" S0 T3 ; display message

Dear All, I hope this message finds you well.
I have a Railcore II 300, with Duet 2Wifi and Duet 5. Firmware version is 3.4.1
I am also using Euclid probe as a bed sensor (pretty good).
The issue for today is with the programing of the orbiter and maybe is something really silly.
At the orbiter filament sensor page, https://orbiterprojects.com/orbiter-filament-sensor/
The setting instructions recommend to add 4 lines of code and 2 macros for the filament sensor to autoload and auto unload the filament.
When I turn the printer and add the filament, the auto load macro turns on and successfully loads the filament. once it finish loading, and without me pressing any button, the filament unloads....
The printer goes in an endless cycle of loading and unloading. What am I doing wrong?

3.2 with Duet 2 Wifi and Duet 5 as extension. Railcore II 300 ZL configuration.

Correct. The M307 goes directly to the config override. I copy it from there an placed it on the config.g
It is working, so I believe it does not hurt to have it twice...
Good printing!

Gents,
I have an ender 5 pro and went through the same learning you are.
Phaedrux helped me to work through it. It is only fair I spread the knowledge.
Here is the section of my config.g file for your reference.
It may not be academically perfect, but copying the tuning values into the config and changing the D value helped.

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T98801 B4185 ; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0 ; create bed heater output on bedheat and map it to sensor 0
M143 H0 S120 ; set temperature limit for heater 0 to 120C
M307 H0 A88.4 C265.5 D2.0 S1.00 V23.9 B0 ; disable bang-bang mode for the bed heater and set PWM limit (Values copied from auto tune D corrected from 0.9 to 2 by Phaedrux)
M140 H0 ; map heated bed to heater 0
M308 S1 P"e0temp" Y"thermistor" T98801 B4185 ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1 ; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S300 ; set temperature limit for heater 1 to 300C
M307 H1 A390.6 C153.8 D3.5 S1.00 V23.9 B0 ; disable bang-bang mode for heater and set PWM limit (Values copied from auto tune)

@arhi
I am attaching a link to a resin vendor for injection molders and other plastic processes containing a table for water content on different polymers as well as a reference on how to measure that.
https://omnexus.specialchem.com/polymer-properties/properties/water-absorption-24-hours

What filaments are interested in making?

@arhi
That is a very good observation. Filaments are made by melting dry polymer in the extruded and pushing them through a die with the proper diameter and then immersed into a water bath to solidify.
The residence time in the bath is enough to chill the filament but not enough to to raise the internal moisture content above 300 ppm.
It takes time to make the moisture diffuse into the polymer.

@Phaedrux
I have not posted in a while and I wanted to thank for all the help received, by posting the latest config for the machine.
Best configuration (so far) working with Simplify 3D. Please uncheck the boxes as per this picture to let the firmware control the printing.

The config is below
; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2.1.8 on Sun Apr 19 2020 17:01:43 GMT-0400 (Eastern Daylight Time)

; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Daniel Ender 5 Duet 2 Wifi" ; set printer name

; Network
M552 S1 ; enable network
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet

; Drives
M569 P0 S0 ; physical drive 0 goes backwards
M569 P1 S0 ; physical drive 1 goes backwards
M569 P2 S0 ; physical drive 2 goes backwards
M569 P3 S1 ; physical drive 3 goes forwards
M584 X0 Y1 Z2 E3 ; set drive mapping
M350 X16 Y16 Z16 E16 I1 ; configure microstepping with interpolation
M92 X80.00 Y80.00 Z811.00 E409.00 ; set steps per mm
M566 X900.00 Y900.00 Z60.00 E4000.00 ; set maximum instantaneous speed changes (mm/min)
M201 X6000.00 Y6000.00 Z60.00 E4000.00 ; set accelerations (mm/s^2)
M203 X15000.00 Y15000.00 Z600.00 E8000.00 ; set maximum speeds (mm/min)
M204 P800 T2000 ; set accel for XY print (P) and travel moves (T).
M207 S0.85 R-0.000 F3200 T2600 Z0.0 ; set firmware retraction
M572 D0 S0.050 ; set pressure advance
M906 X850 Y850 Z850 E850 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X220 Y220 Z300 S0 ; set axis maxima

; Endstops
M574 X2 S1 P"xstop" ; configure active-high endstop for high end on X via pin xstop
M574 Y2 S1 P"ystop" ; configure active-high endstop for high end on Y via pin ystop
M574 Z1 S2 ; configure Z-probe endstop for low end on Z

; Z-Probe
M950 S0 C"exp.heater3" ; create servo pin 0 for BLTouch
M558 P9 C"zprobe.in" H5 F120 T12000 ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X-45 Y3 Z1.95 ; set Z probe trigger value, offset and trigger height
M557 X15:160 Y15:200 S20 ; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T98801 B4185 ; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0 ; create bed heater output on bedheat and map it to sensor 0
M143 H0 S120 ; set temperature limit for heater 0 to 120C
M307 H0 A88.4 C265.5 D2.0 S1.00 V23.9 B0 ; disable bang-bang mode for the bed heater and set PWM limit (Values copied from auto tune D corrected from 0.9 to 2 by Phaedrux)
M140 H0 ; map heated bed to heater 0
M308 S1 P"e0temp" Y"thermistor" T98801 B4185 ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1 ; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S300 ; set temperature limit for heater 1 to 300C
M307 H1 A390.6 C153.8 D3.5 S1.00 V23.9 B0 ; disable bang-bang mode for heater and set PWM limit (Values copied from auto tune)

; Fans
M950 F0 C"fan0" Q500 ; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1 ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"fan1" Q500 ; create fan 1 on pin fan1 and set its frequency
M106 P1 S1 H1 T45 ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 S"E3D V6 Nozzle X" D0 H1 F0 ; define tool 0
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined

; Miscellaneous
M911 S10 R11 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; set voltage thresholds and actions to run on power loss

Enjoy printing!!!