Now I believe the current 2.02 bin file is incorrect, if I upload it to the board it becomes entirely unresponsive

No matter what I do it wont change from the following versions.

Firmware Electronics: Duet WiFi 1.02 or later
Firmware Version: 1.21RC1 (2018-01-25)
WiFi Server Version: 1.21
Web Interface Version: 1.21.2-dc42

it recognizes the bin files and claims to upload them but it lies. I guess now nuke the board and use SAM-BA again?

I am rather confused, I downloaded it from that github but my version is 1.21???... I will get the actual latest version uploaded. As for the reduced current during homing, I will have to do that. thanks for the great suggestion.

re-uploading the DC42 firmware has not changed anything sadly

This is the most recent version available so I'm afraid updating again won't do much. I uploaded with SAM-BA and verified the MD5 hash when downloading to be 100% positive that every last bit was correct. I did this because my (real!) duet arrived in an erased state. For now I am using a nozzle mounted microswitch with a Z offset of 7.18mm and the actual Z height is about 718.55 at room temperature. I only use it for probing, I would like if I could use it to calculate Z also but I haven't seen anything about this FW being able to do such a thing. I just put "safe" values in to prevent a nozzle crash because my Z axis is strong enough to absolutely demolish the machine should it fail to stop at an appropriate distance

I just now noticed the web interface said the "Maximum deviations: -4.265 / -2.827 mm" so I assumed the 4.25 is from the bed height map. I disabled the line "G29 S1 ; Enable" and it now shows the "true" z height value. I will try to get my deviation values lower with some manual leveling to see if it helps that value out... Is that normal or do I have a problem?

Sure! here they are... This is 1.21RC1

; homeall.g
; called to home all axes
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:03 GMT-0800 (Pacific Standard Time)
G91 ; relative positioning
;G1 Z5 F6000 S2 ; lift Z relative to current position
G1 S1 Y-705 F1800 ; move quickly to X or Y endstop and stop there (first pass)
G1 S1 X-780 F1800 ; move quickly to X or Y endstop and stop there (first pass)
G1 S1 Y-705 ; home Y axis
G1 S1 X-780 ; home X axis
G1 X5 Y5 F1000 ; go back a few mm
G1 S1 Y-705 ; then move slowly to Y axis endstop
G1 S1 X-780 F360 ; move slowly to X axis endstop once more (second pass)
;G1 Z-5 F6000 S2 ; lift Z relative to current position
G1 S1 Z723 F1800 ; move Z up stopping at the endstop
G90 ; absolute positioning
;G92 Z718 ; set Z to axis minimum (you may want to adjust this)

; Uncomment the following lines to lift Z after probing
;G91 ; relative positioning
;G1 S2 Z5 F100 ; lift Z relative to current position
;G90

; homex.g
; called to home the X axis
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:04 GMT-0800 (Pacific Standard Time)
G91 ; relative positioning
;G1 Z5 F6000 S2 ; lift Z relative to current position
G1 S1 Y-780 F1800 ; move quickly to y axis endstop and stop there (first pass)
G1 S1 X-780 F1800 ; move quickly to X axis endstop and stop there (first pass)
G1 X5 F6000 ; go back a few mm
G1 S1 X-780 F360 ; move slowly to X axis endstop once more (second pass)
;G1 Z-5 F6000 S2 ; lower Z again
G90 ; absolute positioning

; homey.g
; called to home the Y axis
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:04 GMT-0800 (Pacific Standard Time)
G91 ; relative positioning
;G1 Z5 F6000 S2 ; lift Z relative to current position
G1 S1 Y-705 F1800 ; move quickly to Y axis endstop and stop there (first pass)
G1 Y5 F6000 ; go back a few mm
G1 S1 Y-705 F360 ; move slowly to Y axis endstop once more (second pass)
;G1 Z-5 F6000 S2 ; lower Z again
G90 ; absolute positioning

; homez.g
; called to home the Z axis
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:04 GMT-0800 (Pacific Standard Time)
G91 ; relative positioning
G1 Z5 F6000 S2 ; lift Z relative to current position
G1 S1 Z723 F1800 ; move Z up until the endstop is triggered
;G92 Z718 ; set Z position to axis minimum (you may want to adjust this)

; Uncomment the following lines to lift Z after probing
;G91 ; relative positioning
;G1 S2 Z5 F100 ; lift Z relative to current position
;G90 ; absolute positioning

; bed.g
; called to perform automatic bed compensation via G32
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:03 GMT-0800 (Pacific Standard Time)
M557 X0:775 Y0:700 S36.8
M561 ; clear any bed transform
G29 ; probe the bed and enable compensation

Hello I have been setting up a COREXY with Z max homing but have become stuck in the process because the firmware seems to be wrongly adding 4.25 (or sometimes 4.50) to the Z axis height. I have not done much with the printer beyond running homing and G32 routines, so it's doubtful that I accidentally changed something to cause this... but who knows! My Z probe trigger distance is around 7.2mm, changing that value does not affect anything as far as I can tell. Here's my config file. Thanks for taking a look!

; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2 on Wed Feb 27 2019 21:47:03 GMT-0800 (Pacific Standard Time)

; General preferences
G90 ; Send absolute coordinates...
M83 ; ...but relative extruder moves

M667 S1 ; Select CoreXY mode
G29 S1 ; Enable leveling
; Network
M550 P"Big Printer" ; Set machine name
M551 P"Password" ; Set password
M552 S1 ; Enable network
M587 S"SSID" P"PASSWORD" ; Configure access point. You can delete this line once connected
M586 P0 S1 ; Enable HTTP
M586 P1 S0 ; Disable FTP
M586 P2 S0 ; Disable Telnet

; Drives
M584 X0 Y1 Z2:4 E03 ;Map drive 4 to second Z motor
M569 P0 S1 ; Drive 0 goes forwards
M569 P1 S0 ; Drive 1 goes backwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S0 ; Drive 3 goes BACKWARDS
M350 X32 Y32 Z32 I0 ; Configure microstepping without interpolation
M350 E16 I1 ; Configure microstepping with interpolation
M92 X200.00 Y200.00 Z2400.00 E420.00 ; Set steps per mm
M566 X900.00 Y900.00 Z12.00 E120.00 ; Set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z400.00 E1200.00 ; Set maximum speeds (mm/min)
M201 X100.00 Y100.00 Z20.00 E250.00 ; Set accelerations (mm/s^2)
M906 X800.00 Y800.00 Z1000.00 E800.00 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 X775 Y700 Z700 S0 ; Set axis maxima

; Endstops
M574 X1 Y1 Z2 S0 ; Set active low and disabled endstops

; Z-Probe
M558 P5 I1 H5 F400 T6000 ; Set Z probe type to switch and the dive height + speeds
G31 P500 X0 Y0 Z7 ; Set Z probe trigger value, offset and trigger height
M557 X0:775 Y0:700 S20 ; 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

; Fans
M106 P0 S0 I0 F500 H-1 ; Set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S0 I0 F500 H-1 ; Set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned off

; Tools
M563 P0 D0 H1 ; 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

; Automatic saving after power loss is not enabled

; Custom settings are not configured