@achrn That seems to have fixed most of everything! I implemented what you told me and everything seems to be working, I just had to change the Z offset for my printer to get a good first layer. The extra M558s were part of the original tutorial, and I'm planning on phasing them out after reading up on them a little bit. Although, I do have another peculiar issue. The temperature readings for the PINDA V2 are negative... -26°C when turning on, and when printing they warmed up to around -17°C. Is this an incorrect config, or is the PINDA just done? The M18 was also part of the Firmware provided in the tutorial... I'll look into that as well.

Thank you for the info!

@droftarts Yes, the probe does have a light on it, showing it is getting power, and it turns off when the probe is triggered. Everything is wired as such, and there is continuity in the wires:

When triggered the probe shows 1000, when not 0. I don't know where to look to find the thermistor readings of the Pinda sensor. Putting something metal under the sensor shoes it triggering correctly both on the sensor itself and in DWC. And after looking closely, it does seem that the probe is triggered before the probing move and the probe never triggers on the next probing move. But why? the bed nor X axis seem to be that badly out of alignment. After lowering it down to were the probe triggers, moving it to the other side does seems to stop it from triggering, but this issue seems to be very small. Isn't this compensation in place to fix just this?

With M18, its just a bit bizarre that that wasn't in the software from the RR config tool... / CNC Kitchen's tutorial. Would setting it to zero be the right thing to put there? What is an extruder drive number?

Sorry for the delay, Thank you!

I am rebuilding a Prusa mk2.5s to use a duet 3 mini 5+. I am using a bulk of the code from CNCkitchen's guide but I changed some of the probe settings according to this forum.
This left me with this config file:

; Configuration file for Duet 3 Mini 5+ (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Mon Mar 15 2021 19:09:36 GMT+0100 (Mitteleuropäische Normalzeit)

; ##### General preferences
M575 P1 S1 B57600                                                   ; enable support for PanelDue
G90                                          						; send absolute coordinates...
M83                                          						; ...but relative extruder moves
M550 P"Prusa MK2.5S DUET"                          					; set printer name

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

; ##### 12864 Menu
M918 P2 E-4

; ##### Drives
M569 P1 S0 D3 V10                                					; X drive @1
M569 P2 S0 D3 V10                                					; Y drive @2
M569 P0 S0 D3 V100                               					; Z left drive @0
M569 P4 S0 D3 V100                               					; Z right drive  @4
M569 P3 S1 D3 V0                                					    ; E drive @3 - inversed
M584 X1 Y2 Z0:4 E3                     								; set drive mapping
M671 X-37:287 Y0:0 S10                                     			; define dual driven z-axis 

M350 X16 Y16 Z16 E16 I1                      						; configure microstepping with interpolation
M92 X100.00 Y100.00 Z400.00 E140.00             					; set steps per mm
M566 X600.00 Y600.00 Z48.00 E300.00        							; set maximum instantaneous speed changes (mm/min)
M203 X8000.00 Y8000.00 Z720.00 E7200.00      						; set maximum speeds (mm/min)
M201 X1250.00 Y1250.00 Z1250.00 E2000.00        					; set accelerations (mm/s^2)
M906 X750 Y750 Z600 E700 I30                						; set motor currents (mA) and motor idle factor in per cent
M84 S30                                      						; Set idle timeout

; ##### Axis Limits
M208 X0 Y-4 Z0 S1                             						; set axis minima
M208 X255 Y212.5 Z215 S0                       						; set axis maxima

; ##### Endstops
M574 X1 S1 P"io5.in"                        						; X endstop
M574 Y1 S1 P"io1.in"                        						; Y endstop

; ##### Filament Sensor
M591 D0 P2 C"io3.in" S1                                    			; Filament Runout Sensor

; ##### Z-Probe Settings for PINDA 2
M558 P8 C"io2.in" H1 F1000 T6000 A3              				; Prusa PindaV2 Endstop
M308 S2 P"temp2" A"Pinda V2" Y"thermistor" T100000 B3950      		; Prusa PindaV2 Thermistor
;G31 P500 X23 Y5 Z1.4 S21 H2 T0.02                         			; Nozzle offset - Powder Coated Sheet with temperature compensation (0.02mm/°C)
G31 P500 X23 Y5 Z1.1 S21 H2 T0.02                                    			; Nozzle offset - Smooth Sheet
M574 Z1 S2                                                 			; Set Z axis endstop, controlled by probe
M557 X24:228 Y6:210 P5                                    			; Define mesh grid for probing
M376 H5																; Fade height 5mm

; ##### Heaters
; Bed Heater
M308 S0 P"temp1" Y"thermistor" B4725 C7.060000e-8 					; configure sensor 0 as thermistor on pin temp1
M950 H0 C"out0" Q25 T0                           					; create bed heater output on out0 and map it to sensor 0, PWM frequency: 25Hz
M307 H0 R0.262 C338.0 D10.52 S1.00 V11.8 B0							; Bed tuning values, enable PID
M140 H0                                                    			; Bed uses Heater 0
M143 H0 S120                                               			; Set temperature limit for heater 0 to 120C Bed
; Hotend heater
M308 S1 P"temp0" Y"thermistor" B4725 C7.060000e-8 					; configure sensor 1 as thermistor on pin temp0
M950 H1 C"out1" T1                           						; create nozzle heater output on out1 and map it to sensor 1
M307 H1 B0 S1.00                             						; disable bang-bang mode for heater  and set PWM limit
M143 H1 S295                                 						; set temperature limit for heater 1 to 295C
M302 S170 R170                                         				; allow extrusion starting from 170°C and retractions already from 170°C

; ##### Fans
; Part cooling fan
M950 F0 C"out3" Q100                         						; create fan 0 on pin out3 and set its frequency
M106 P0 S0 H-1                               						; set fan 0 value. Thermostatic control is turned off
; Hotend cooling fan
M950 F1 C"out6" Q5000												; NOCTUA fan an pin out6 with 5000Hz PWM frequency
M106 P1 T55 S255 H1  												; Temperature control: turn fan on at 55°C

; ##### Tools
M563 P0 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
M572 D0 S0.06								 						; Pressure Advance

; ##### Startup
M18 XYE0                                                				; release / unlock X, Y, and E axis
M501                                                   				; use config-override (for Thermistor Parameters and other settings)
G90                                                    				; send absolute coordinates...
M83                                                   				; ... but relative extruder moves

And this is how my bed.g file looks currently (theres a pretty good explenation as to why it is like this in this forum) :

; called to perform automatic bed compensation via G32
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Mon Mar 15 2021 19:09:36 GMT+0100 (Mitteleuropäische Normalzeit)
M561                                                       ; Clear any existing bed transform.
G28 ; home
G1 Z220 F10000
M558 F10000
G30

M558 F100 A5 S0.003
G30 P0 X25 Y105 Z-99999 ; probe near a leadscrew, half way along Y axis
G30 P1 X215 Y105 Z-99999 S2 ; probe near a leadscrew and calibrate 2 motors

M558 F200 A1

G1 X10 Y210 Z10 F10000

But, when I run bed.g, the printer says this error after going to the first probing point: "Error: Probe already triggered at start of probing move" and then, at the second probing point it has this error: "Error: Probe was not triggered during probing move". This also occurs when I try to run the mesh bed compensation via G29, the printer goes to the first probing point and then says Error: Probe already triggered at start of probing move, stopping there and doing nothing else. I have tried to fix this issue, but I can't find any solution or reason as to why it's doing what it's doing. So here I am now...

Side note: In CNCKitchen's original files, in the config.g file, on line 87, it said M18 XYE. But, whenever I tried to save the config, the board said this:

M98 P"config.g"
HTTP is enabled on port 80
FTP is disabled
TELNET is disabled
Error: in file macro line 87 column 8: M18: expected number after 'E'

So, I changed it to the current "M18 XYE0", which resulted in the board saying this instead:

M98 P"config.g"
HTTP is enabled on port 80
FTP is disabled
TELNET is disabled

Does this matter?

Thank you for your time and help