Shooting around here
With what im trying to achieve described
M950 J1 C"^e0stop"; that would from my understanding turn my e0stop to a general purpose input pin using a pull up resistor which from a quick google search which creates a signal from the lack of input signal. Am I on the right track with that?

@OwenD it's not a on off switch that I described first. It is the square wave pulse type. When im adding code like this to the config.g is there a certain place it belongs?
I've only been changing existing code to fit my needs I haven't really successfully added my own code yet.
I didn't run my pump from from my duet because my input voltage is 24v to duet and my fan and water pump were 12v so it's wired live all the time to a 12v converter.
I really want the flow sensor to pause the program if theres no pulse signal and shut down my hot end in the event of lost coolant and/or pump failure.

I am running a dyze designs water cooled hot end and I decided to buy a flow switch so I could code the printer to if for some reason the pump fails. I have the water cooled system done entirely independent so if something there fails, the duet would unsuspectingly run the printer to destruction I assume. Possible destroyed printer, potential house fire.. Not my thing so for piece of mind, I got a flow switch.
Repinned the connector when it showed up and it plugged right into the duet board. Awesome. I am noticing that it might be just barely too big for my pump though because im getting major switch bounce. It seems like im picking up the pulses from the pump.
I tried wiring in a small capacitor in an effort to "charge and maintain" the signal but it didn't quite seem to work like I figured. Turns out my switch isn't really a on off switch as I thought. The switch produces a alternating current and I guess the board is supposed to interpret the pulses as flow? Is this something I can use for this application?

@droftarts wow! Simple fix I guess I just assumed since the light was coming on the board they were working. Got all the axis aligned right and switched the end stops with the ! In the config.g
The other board must be fine good thing I have another printer laying around to use it on so it's not a waste
Sure appreciate the help!

I also clearly misunderstood how to add the files in the little scroll box

bought a cube pro duo that seemed to be somebody's project. it was fitted with a dyze design extruder and hotend and came with two duet boards and listed as "just needs put together" ...... so here we are. the board that was in it when i got it was a duet 2 wifi clone that i thought was having issues when i got everything wired i go to home the all the home buttons control 1 axis and it was ignoring the endstop signal and would just crash the machine. it seems like the code that the steppers are receiving from the duet board just dont seem to match at all what is being commanded.
then i bought a brand new duet 2 wifi from matter hackers and i get it all wired up, and set up with the setup tool and im running into very similar issues. ill run the home x file for instance and what happens is the z axis moves up 10mm or so, y carriage rapid moves 5mm over then the z goes back down to original position. then ill click home y file and the same exact moves will happen.. home z differs only in the fact that it has a 20mm movement up with no retraction at all. new board came with 3.1 installed which i couldn't get working so i update to the new 3.4 and still having the same issues. i'm confused and need a different set of eyes on this problem
i can after the axis thinks its homed can control manually by typing in gcode at the top of the dashboard and that does exactly as commanded

; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.3.16 on Mon Jun 12 2023 18:37:32 GMT-0500 (Central Daylight Time)

; General preferences
G90                                                ; send absolute coordinates...
M83                                                ; ...but relative extruder moves
M550 P"plastibot"                                  ; set printer name

; Network
M551 P"7852492036"                                 ; set password
M552 S1                                            ; enable network
M586 P0 S1                                         ; enable HTTP
M586 P1 S0                                         ; disable FTP
M586 P2 S0                                         ; disable Telnet

; Drives
M569 P0 S1                                         ; physical drive 0 goes forwards
M569 P1 S1                                         ; physical drive 1 goes forwards
M569 P2 S1                                         ; physical drive 2 goes forwards
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 Z400.00 E420.00                  ; set steps per mm
M566 X900.00 Y900.00 Z60.00 E120.00                ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z180.00 E1200.00            ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z20.00 E250.00                ; set accelerations (mm/s^2)
M906 X800 Y800 Z800 E800 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 X230 Y210 Z200 S0                             ; set axis maxima

; Endstops
M574 X1 S1 P"xstop"                                ; configure switch-type (e.g. microswitch) endstop for low end on X via pin xstop
M574 Y1 S1 P"ystop"                                ; configure switch-type (e.g. microswitch) endstop for low end on Y via pin ystop
M574 Z1 S1 P"zstop"                                ; configure switch-type (e.g. microswitch) endstop for low end on Z via pin zstop

; Z-Probe
M558 P0 H5 F120 T6000                              ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:195 S20                           ; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B4138     ; 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
M307 H0 B0 S1.00                                   ; disable bang-bang mode for the bed heater and set PWM limit
M140 H0                                            ; map heated bed to heater 0
M143 H0 S120                                       ; set temperature limit for heater 0 to 120C
M308 S1 P"e0temp" Y"thermistor" T100000 B4138      ; 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
M307 H1 B0 S1.00                                   ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S480                                       ; set temperature limit for heater 1 to 480C

; 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 P1 D0 H1 F0                                   ; define tool 1
G10 P1 X0 Y0 Z0                                    ; set tool 1 axis offsets
G10 P1 R0 S0                                       ; set initial tool 1 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

; homex.g
; called to home the X axis
;
; generated by RepRapFirmware Configuration Tool v3.3.16 on Mon Jun 12 2023 18:37:32 GMT-0500 (Central Daylight Time)
G91               ; relative positioning
G1 H2 Z5 F6000    ; lift Z relative to current position
G1 H1 X-235 F1800 ; move quickly to X axis endstop and stop there (first pass)
G1 H2 X5 F6000    ; go back a few mm
G1 H1 X-235 F360  ; move slowly to X axis endstop once more (second pass)
G1 H2 Z-5 F6000   ; lower Z again
G90               ; absolute positioning

m98 p"config.g"
HTTP is enabled on port 80
FTP is disabled
TELNET is disabled
ok

this is all the info i get back on this with m98. i see others on here getting back the whole config.g file. could this be part of my issue??