@Phaedrux I am using E16 now for micro stepping. And eSteps value was from the previous board calibration. I figured it was a good starting point before doing a new esteps calibration.
I had been swapping cables on the motor side for testing as its just easier, but just now I swapped them at the board side and the issue didnt follow the driver this time, so I am pretty sure its the cable. Didnt realize Buy Once Cry Once applied to stepper motor cables 
It was working for a moment, then stopped again.
At this point I am thinking its something physical. I am going to order some "decent" cables as while new, they were the cheapest cables off of amazon that would get to me next day. So while statistically unlikely I'd have 3 flaky cables, I suppose its possible when you get the cheapest China has to offer.
So unless you see something else in the config, I am going to order a new cable and try again. Will probably be a couple of days.
I think I see what I did that changed the behavior, i accidently loaded the incorrect extruder microstepping when tinkering with it last evening. I am setting that back to 16 and am trying again.
Here is my config
; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Mon Mar 01 2021 16:45:00 GMT-0500 (Eastern Standard Time)
; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"Ender5 Plus" ; set printer name
;G31 4.65 ; Z home height
M208 X0:350 Y0:350 ; X carriage moves from 0 to 350, Y bed goes from 0 to 350
; Network
M552 S1 ; enable network
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet
; Drives
; 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 S0 ; physical drive 3 goes backwards
M569 P4 S0 ; physical drive 4 goes backwards
M584 X0 Y1 Z2 E3 ; set drive mapping
M671 X0:300 Y130 S10 ; leadscrews at left (connected to Z) and right (connected to E1) of X axis
M350 E256 I0 ; configure microstepping without interpolation
M350 X16 Y16 Z16 I1 ; configure microstepping with interpolation
M92 X80.00 Y80.00 Z400.00 E139.64 ; 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 X350 Y350 Z400 S0 ; set axis maxima
; Endstops
M574 X1 S1 P"xstop" ; configure active-high endstop for low end on X via pin xstop
M574 Y1 S1 P"ystop" ; configure active-high endstop for low end on Y via pin ystop
M574 Z1 S2 ; configure Z-probe endstop for low end on Z
; Z-Probe
M950 S0 C"exp.heater7" ; create servo pin 0 for BLTouch
M558 P9 C"^zprobe.in" H5 F120 T6000 ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X0 Y0 Z2.5 ; set Z probe trigger value, offset and trigger height
M557 X15:315 Y15:320 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 R0.187 C662.4 D6.08 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 R2.834 C115.9 D3.45 S1.00 V24.0 ; disable bang-bang mode for heater and set PWM limit
M143 H1 S280 ; set temperature limit for heater 1 to 280C
; 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 H-1 ; set fan 1 value. Thermostatic control is turned off
; Tools
M563 P0 D0 H1 F0:1 ; define tool 0
G10 P0 X0 Y0 Z2.5 ; 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
M575 P1 S1 B57600 ; enable support for PanelDue
Ok, this is just getting weird, after letting it sit over night off, i turned it on to get the results you asked for, and its working kinda again. Now its extruding but real slow and when you ask for 100mm you get like 6mm.
One of the first things I did is swapped the cable and the new cable showed the same results. And I tried swapping the X and E cables, the X started showing the same behavior.
I purchased it from Digitmakers.ca on 2/15, I am in the US, just that was the closest retailer with inventory on hand. Just got around to wiring it up this week.
m122
=== Diagnostics ===
RepRapFirmware for Duet 2 WiFi/Ethernet version 3.2.2 running on Duet WiFi 1.02 or later
Board ID: 0JD0M-9P6M2-NW4SN-6J1DG-3S86N-TAT3L
Used output buffers: 3 of 24 (16 max)
=== RTOS ===
Static ram: 23460
Dynamic ram: 73376 of which 52 recycled
Never used RAM 15192, free system stack 115 words
Tasks: NETWORK(ready,164) HEAT(blocked,308) MAIN(running,449) IDLE(ready,20)
Owned mutexes: WiFi(NETWORK)
=== Platform ===
Last reset 00:05:37 ago, cause: software
Last software reset at 2021-03-06 11:07, reason: User, GCodes spinning, available RAM 15192, slot 0
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0041f000 BFAR 0xe000ed38 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
Aux0 errors 3,3,3
MCU temperature: min 18.6, current 21.3, max 21.6
Supply voltage: min 23.4, current 23.5, max 24.3, under voltage events: 0, over voltage events: 0, power good: yes
Driver 0: position 10000, standstill, SG min/max 0/120
Driver 1: position 14000, standstill, SG min/max 0/463
Driver 2: position 3000, standstill, SG min/max not available
Driver 3: position 0, standstill, SG min/max not available
Driver 4: position 0, standstill, SG min/max not available
Driver 5: position 0
Driver 6: position 0
Driver 7: position 0
Driver 8: position 0
Driver 9: position 0
Driver 10: position 0
Driver 11: position 0
Date/time: 2021-03-06 11:13:27
Cache data hit count 407538838
Slowest loop: 9.37ms; fastest: 0.18ms
I2C nak errors 0, send timeouts 0, receive timeouts 0, finishTimeouts 0, resets 0
=== Storage ===
Free file entries: 10
SD card 0 detected, interface speed: 20.0MBytes/sec
SD card longest read time 4.4ms, write time 0.0ms, max retries 0
=== Move ===
DMs created 83, maxWait 62981ms, bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves 22, completed moves 22, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 14], CDDA state -1
=== AuxDDARing ===
Scheduled moves 0, completed moves 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== Heat ===
Bed heaters = 0 -1 -1 -1, chamberHeaters = -1 -1 -1 -1
Heater 0 is on, I-accum = 0.7
Heater 1 is on, I-accum = 0.6
=== GCodes ===
Segments left: 0
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
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
Daemon is idle in state(s) 0
Autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 18.96ms; fastest: 0.00ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0), 0 sessions
HTTP sessions: 1 of 8
I just got a Duet Wifi to upgrade an Ender 5 Plus with. It was a working machine when it was disassembled. I have wired everything but the extruder driver feels super "weak" it is a Creality 42-40 stepper rated at 1.5 A. However I tried bumping the current up higher all the way up to 1500 and it just kinda "shivvers" when it tries to move, even when there is no filament.
I switched the extruder to the E1 driver and changed the mapping and it works just fine.
Being that this is a new board it appears that the E0 extruder driver is defective. I am mostly posting this as the duet page said for warranty return you need to post a thread.
Let me know what if anything i should try, but the exact same settings worked for E1 where as the E0 driver just twitches.