If anybody else is reading this and having the same troubles I will be back to post my methods for getting everything working. At the moment I have had some troubles with upgrading from 2.x to 3.x, that's now sorted, but it has messed with my configuration. Some of the axis don't respond, the probe still doesn't register and the axis that do work are reversed (even reversing the direction in config.g doesn't solve the issue). I have a few weeks of freelance work before I can get back to it.

M122

=== Diagnostics ===
RepRapFirmware for Duet 2 WiFi/Ethernet version 2.03beta3 running on Duet WiFi 1.02 or later
Board ID: 0JD0M-9P6M2-NW4SS-6JKFD-3SD6N-KUZBL
Used output buffers: 1 of 20 (10 max)
=== RTOS ===
Static ram: 25632
Dynamic ram: 93680 of which 0 recycled
Exception stack ram used: 276
Never used ram: 11484
Tasks: NETWORK(ready,652) HEAT(blocked,852) MAIN(running,3816) IDLE(ready,196)
Owned mutexes:
=== Platform ===
Last reset 00:03:01 ago, cause: power up
Last software reset at 2021-02-05 20:20, reason: User, spinning module GCodes, available RAM 11356 bytes (slot 1)
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0441f000 BFAR 0xe000ed38 SP 0xffffffff Task 0x4e49414d
Error status: 0
Free file entries: 10
SD card 0 detected, interface speed: 20.0MBytes/sec
SD card longest block write time: 0.0ms, max retries 0
MCU temperature: min 24.6, current 26.7, max 26.8
Supply voltage: min 12.4, current 12.5, max 12.5, under voltage events: 0, over voltage events: 0, power good: yes
Driver 0: standstill, SG min/max not available
Driver 1: standstill, SG min/max not available
Driver 2: standstill, SG min/max not available
Driver 3: standstill, SG min/max not available
Driver 4: standstill, SG min/max not available
Date/time: 2021-02-05 20:27:09
Cache data hit count 646318362
Slowest loop: 2.08ms; fastest: 0.07ms
I2C nak errors 0, send timeouts 0, receive timeouts 0, finishTimeouts 0
=== Move ===
Hiccups: 0, FreeDm: 169, MinFreeDm: 169, MaxWait: 0ms
Bed compensation in use: none
Bed probe heights: 0.000 0.000 0.000 0.000 0.000
=== MainDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0
=== Heat ===
Bed heaters = 0 -1 -1 -1, chamberHeaters = -1 -1
Heater 1 is on, I-accum = 0.0
=== GCodes ===
Segments left: 0, aux move: no
Stack records: 1 allocated, 0 in use
Movement lock held by null
http is idle in state(s) 0
telnet is idle in state(s) 0
file is idle in state(s) 0
serial is idle in state(s) 0
aux is idle in state(s) 0
daemon is idle in state(s) 0
queue is idle in state(s) 0
autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 15.44ms; fastest: 0.00ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0) Telnet(0)
HTTP sessions: 1 of 8

• WiFi -
  Network state is running
  WiFi module is connected to access point
  Failed messages: pending 0, notready 0, noresp 0
  WiFi firmware version 1.23
  WiFi MAC address 24:a1:60:2f:8c:06
  WiFi Vcc 3.33, reset reason Turned on by main processor
  WiFi flash size 4194304, free heap 23648
  WiFi IP address 172.20.10.2
  WiFi signal strength -65dBm, reconnections 0, sleep mode modem
  Socket states: 0 0 0 0 0 0 0 0

M98 P"config.g"

HTTP is enabled on port 80
FTP is disabled
TELNET is disabled
Warning: M308 command is not supported
Warning: M950 command is not supported

Oh I was sure it was NPN. I'm just very new to Duet and there's a lot of info I'm having to juggle. So I may not be putting my point across properly.

I have 12v feeding the sensor, can the Z probe in handle that voltage? I'm not entirely sure what an NPN outputs on its signal wire.

Sorry, I must've deleted that from my last reply.

M119
Endstops - X: at min stop, Y: at min stop, Z: not stopped, Z probe: at min stop

I'm wondering if it may be that I'm using the wrong diode from the Probe in

The motors weren't engaging with ! but they've started working with the version 2 I1

My probe isn't always triggered. It will trigger (LED on) when it senses the bed, as you would expect. I've checked the wiring for the Z probe multiple times but I will have a triple check.

I've managed to get the Z axis motors working with the following change..
I have an NO probe, so M558 required the "I1" command to invert the signal

M558 P4 C"^zprobe.in" H5 F120 T6000

changed to

M558 P4 C"^zprobe.in" I1 H5 F120 T6000

Now I'm still left with the issue of the probe recognising the bed (LED lights up when it's close enough) but the board not telling the motors to disengage.

M119
Endstops - X: at min stop, Y: at min stop, Z: not stopped, Z probe: at min stop

Thanks for your answer but I'm still getting the same issue after that change.

To those with experience adding a Duet 2 Wifi to the Anet A8...
I have a Z homing issue. I can happily home X and Y, the Z motor will even move slightly while I'm homing those axis, so I know the motors are getting a signal from the board.
When I come to home the Z axis I get the error :

"G28 Z Error: Z probe already triggered at start of probing move"

I've included my wiring set up and config.g

; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.2 on Wed Feb 03 2021 17:45:53 GMT+0000 (GMT)
; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Anet A8" ; set printer name
; Network
M551 P"[password]" ; 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 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 X100.00 Y100.00 Z400.00 E100.00 ; set steps per mm
M566 X600.00 Y600.00 Z18.00 E300.00 ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z180.00 E6000.00 ; set maximum speeds (mm/min)
M201 X1500.00 Y1500.00 Z100.00 E10000.00 ; set accelerations (mm/s^2)
M906 X500 Y500 Z500 E800 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout
; Axis Limits
M208 X-33 Y-10 Z0 S1 ; set axis minima
M208 X220 Y220 Z240 S0 ; set axis maxima
; Endstops
M574 X1 S0 P"xstop" ; configure active-low endstop for low end on X via pin xstop
M574 Y1 S0 P"ystop" ; configure active-low endstop for low end on Y via pin ystop
M574 Z0 S0 ; configure Z-probe endstop for low end on Z
; Z-Probe
M558 P5 C"!^zprobe.in" H5 F120 T6000 ; set Z probe type to switch and the dive height + speeds
G31 P500 X25 Y40 Z2.5 ; set Z probe trigger value, offset and trigger height
M557 X20:200 Y20:200 S40 ; define mesh grid
; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B4725 C7.06e-8 ; 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 S130 ; set temperature limit for heater 0 to 130C
M308 S1 P"e0temp" Y"thermistor" T100000 B4725 C7.06e-8 ; 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 S275 ; set temperature limit for heater 1 to 275C
; 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 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
T0 ; select first tool