Some good news but also some bad news.
Everything is working so to speak. Ran the first print, and I am getting layer shift on the X and Y axis on every layer. Different prints different direction.
I am using Ideamaker as the slicer, I do not think this is the issue, but it is information.
The X and Y axis are still controlled by the integrated steppers.
As the print continues it gets progressively worse.
See below for the config file.
; Configuration file for Duet WiFi (firmware version 2.03)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2.0.4 on Tue Sep 24 2019 14:17:15 GMT+1000 (Australian Eastern Standard Time)
; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Unicorns are not Fucking Real" ; set printer name
; Network
M552 P192.168.1.14 S1 ; enable network and set IP address
M553 P255.255.255.0 ; set netmask
M554 P192.168.1.1 ; set gateway
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet
; Drives
M569 P5 S1 ; physical drive 5 goes forwards
M569 P6 S0 ; physical drive 6 goes backwards
M569 P2 S1 ; physical drive 2 goes forwards
M569 P3 S1 ; physical drive 3 goes forwards
M569 P4 S1 ; physical drive 4 goes forwards
M584 X5 Y6 Z2 E3:4 ; set drive mapping
M350 X16 Y16 Z16 E16:16 I1 ; configure microstepping with interpolation
M92 X128.25 Y128.25 Z1600.00 E425.00:425.00 ; set steps per mm
M566 X900.00 Y900.00 Z12.00 E120.00:120.00 ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z300.00 E1200.00:1200.00 ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z5.00 E250.00:250.00 ; set accelerations (mm/s^2)
M906 X1000 Y1000 Z1600 E800:800 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 X1000 Y1000 Z500 S0 ; set axis maxima
; Endstops
M574 X1 Y1 Z1 S0 ; set active low and disabled endstops
; Z-Probe
M558 P0 H2 F120 T6000 ; disable Z probe but set dive height, probe speed and travel speed
M557 X100:800 Y100:800 S200 ; define mesh grid
; Heaters
M140 H-1 ; disable heated bed
M305 P1 T100000 B4138 R4700 ; set thermistor + ADC parameters for heater 1
M143 H1 S280 ; set temperature limit for heater 1 to 280C
M305 P2 T100000 B4138 R4700 ; set thermistor + ADC parameters for heater 2
M143 H2 S280 ; set temperature limit for heater 2 to 280C
; Fans
M106 P0 S1 I0 F500 H1 T45 ; set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned on
M106 P1 S1 I0 F500 H2 T45 ; set fan 1 value, PWM signal inversion and frequency. 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
M563 P1 D1 H2 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