Thanks again. Happily printing now.

Decided I had nothing to lose and redid the configuration with the RRF configuration tool. This has sorted out all my problems. Thanks for your time David.

Thanks for the input guys. The end stops are 3 wire Makerbot. I am also getting an error on the bed heater.
Error: Temperature reading fault on heater 0: unknown temperature sensor channel
M574 reports Endstop configuration: X:low end unknown type Y: low end unknown type Z: none,

Also getting an error message when connecting on WiFi "Can't open 0:/sys/oem.json to read, error code 4"

I should of said end stops still not stopping X and Y axis and z still getting Insufficient axes homed for bed probing error

The end stops are mechanical except for the IR probe on Z. I have upgraded to 1.2. Now the end stops in Machine properties are hitting but the Z probe has stopped hitting however the red LED on the IR probe is still activating at the right distance from the bed.

Awesome response as usual David. Will do the 1.2 upgrade. In the meantime here is config .g.

; Configuration file for Duet WiFi (firmware version 1.16)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool on Sat Dec 17 2016 11:00:47 GMT+1300 (New Zealand Standard Time)

; General preferences
M111 S0 ; Debugging off
G21 ; Work in millimetres
G90 ; Send absolute coordinates…
M83 ; ...but relative extruder moves
M555 P2 ; Set firmware compatibility to look like Marlin

M667 S1 ; Select CoreXY mode
M208 X0 Y0 Z0 S1 ; Set axis minima
M208 X300 Y300 Z350 S0 ; Set axis maxima

; Endstops
M574 X1 Y1 Z0 S0 ; Define active low and unused microswitches
M558 P1 X0 Y0 Z1 H5 F120 T6000 ; Set Z probe type to unmodulated, the axes for which it is used and the probe + travel speeds
G31 P500 X0 Y0 z1.76 ; Set Z probe trigger value, offset and trigger height

; Drives
M569 P0 S0 ; Drive 0 goes backwards
M569 P1 S1 ; Drive 1 goes backwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S1 ; Drive 3 goes forwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X160 Y160 Z3200 E422 ; Set steps per mm
M566 X900 Y900 Z12 E120 ; Set maximum instantaneous speed changes (mm/min)
M203 X6000 Y6000 Z500 E1200 ; Set maximum speeds (mm/min)
M201 X500 Y500 Z250 E250 ; Set accelerations (mm/s^2)
M906 X1700 Y1700 Z1700 E750 I30 ; Set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Heaters
M143 S300 ; Set maximum heater temperature to 260C
;M305 P0 T100000 B3950 R4700 ; Set thermistor + ADC parameters for heater 0
M305 P1 X200 ; Set thermistor + ADC parameters for heater 1 and remap it to channel 200

; Tools
M563 P0 D0 H1 ; Define tool 0
G10 P0 X0 Y0 ; Set tool 0 axis offsets
G10 P0 R0 S0 ; Set initial tool 0 active and standby temperatures to 0C

; Network
M550 PMy printer ; Set machine name
M552 P0.0.0.0 S1 ; Enable network and acquire dynamic address via DHCP
M501

; Fans
M106 P0 S0.3 I0 F500 H-1 ; Set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S1 I0 F500 H1 T45 ; Set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned on
M106 P2 S1 I0 F500 H1 T45 ; Set fan 2 value, PWM signal inversion and frequency. Thermostatic control is turned on

; Custom settings are not configured

The end stops are being triggered in Machine properties but not stopping the motors. And I am getting an error message on the IR Z probe "Insufficient axes homed for bed probing". I expect it is my bad, but cannot work it out. I tried changing the ends in M557 but no luck. Here are the home files.

; homeall.g
; called to home all axes
;
; generated by RepRapFirmware Configuration Tool on Sat Dec 17 2016 11:00:47 GMT+1300 (New Zealand Standard Time)

; Relative positioning
G91

; Lift Z
G1 Z5 F6000

; Move towards X and Y axis endstops (first pass)
G1 X-305 Y-305 F1800 S1

; Go back a few mm
G1 X5 Y5 F6000

; Move slowly to axis endstops once more (second pass)
G1 X-305 Y-305 F360 S1

; Absolute positioning
G90

; Go to first bed probe point and home the Z axis
G1 X150 Y135 F6000
G30

; Uncomment the following line to lift the nozzle after probing
;G1 Z5 F100

; homex.g
; called to home the X axis
;
; generated by RepRapFirmware Configuration Tool on Sat Dec 17 2016 11:00:47 GMT+1300 (New Zealand Standard Time)

; Lift Z relative to current position
G91
G1 Z5 F6000
G90

; Move quickly to X axis endstop and stop there (first pass)
G1 X-305 F1800 S1

; Go back a few mm
G91
G1 X5 F6000
G90

; Move slowly to X axis endstop once more (second pass)
G1 X-305 F360 S1

; Lower Z again
G91
G1 Z-5 F6000
G90

; homey.g
; called to home the Y axis
;
; generated by RepRapFirmware Configuration Tool on Sat Dec 17 2016 11:00:47 GMT+1300 (New Zealand Standard Time)

; Lift Z relative to current position
G91
G1 Z5 F6000
G90

; Move quickly to Y axis endstop and stop there (first pass)
G1 Y-305 F1800 S1

; Go back a few mm
G91
G1 Y5 F6000
G90

; Move slowly to X axis endstop once more (second pass)
G1 Y-305 F360 S1

; Lower Z again
G91
G1 Z-5 F6000
G90

; homez.g
; called to home the Z axis
;
; generated by RepRapFirmware Configuration Tool on Sat Dec 17 2016 11:00:47 GMT+1300 (New Zealand Standard Time)

; Lift Z relatively to current position
G91
G1 Z5 F6000

; Back to absolute positioning
G90

; Go to first bed probe point and home the Z axis
G1 X20 Y30 F6000
G30

; Uncomment the following lines to lift Z after probing
G91
G1 Z5 F100
G90

I'm running a similar motor on Z axis in my Core XY. It is working fine at 1.8 amps. I did get an external stepper driver in case I needed to go over the 2 amp Duet limit. I'm pretty sure that a Nema 17 would have had enough power for my Z though.

Great thanks dc42 that's done the trick.