Thank you both for your help so far. I'm able to manually home with both of your suggestions, and have found that the reason for the separate moves on the Z motors was due to the motors moving out of sync. Upon moving in the Z direction one motor moves ahead of the other, causing the X gantry to come down on one side; then the other motor follows. Below is a quick photo of my printer. Do you think my issue is because of the Z motors being placed in different positions, or could it still be a configuration issue?

Thanks so much for helping me get this off the ground.

EDIT:

I figured it out! My Z leadscrew steps per mm were completely incorrect. The firmware was set for 5mm leadscrews & needed to be manually adjusted before uploading to the RAMPS board. Sorry for taking up your time. I appreciate your help though. Now on to configuring the BLTouch...

I'm not clear about what isn't working for you. I explained that the standard homing files raise Z by 5mm before homing X and Y. Is the problem that the Z motors are not turning by the same amount?

Yes, sorry for not making that more clear. ZA moves up with Y & ZB moves up with X. They do not move together. I will however attempt your suggestion & post results.

The supply voltage to the board is 12V 30A.

My config.g & homex.g files follow. I copied the values over from a Marlin 1.1.0 RC3 config file. Is the gcode syntax at least correct? Feel free to let me know if I'm asking too much. Also let me know if I should be providing more details.

config.g:

; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v2 on Thu Feb 14 2019 01:42:49 GMT-0600 (Central Standard Time)

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

; Network
M550 P"Pegasus 12"                                 ; Set machine name
M552 S1                                            ; Enable network
M587 S"REDACTED" P"REDACTED"       ; 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
M569 P0 S1                                         ; Drive 0 goes forwards
M569 P1 S1                                         ; Drive 1 goes forwards
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 X80.00 Y80.00 Z4000.00 E500.00                 ; Set steps per mm
M566 X900.00 Y900.00 Z18.00 E120.00                ; Set maximum instantaneous speed changes (mm/min)
M203 X18000.00 Y18000.00 Z300.00 E1500.00          ; Set maximum speeds (mm/min)
M201 X3000.00 Y3000.00 Z100.00 E10000.00           ; Set accelerations (mm/s^2)
M906 X800.00 Y800.00 Z800.00 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 X303 Y328 Z342 S0                             ; Set axis maxima

; Endstops
M574 X1 Y1 S1                                      ; Set active high endstops

; Z-Probe
M574 Z1 S2                                         ; Set endstops controlled by probe
M307 H5 A-1 C-1 D-1                                ; Disable heater on PWM channel for BLTouch
M558 P9 H5 F120 T6000                              ; Set Z probe type to bltouch and the dive height + speeds
G31 P500 X-33 Y0 Z2.5                              ; Set Z probe trigger value, offset and trigger height
M557 X15:0 Y15:195 S20                             ; Define mesh grid

; Heaters
M307 H0 B0 S1.00                                   ; Disable bang-bang mode for the bed heater and set PWM limit
M305 P0 T100000 B4138 R4700                        ; Set thermistor + ADC parameters for heater 0
M143 H0 S150                                       ; Set temperature limit for heater 0 to 150C
M305 P1 T100000 B4138 R4700                        ; Set thermistor + ADC parameters for heater 1
M143 H1 S275                                       ; Set temperature limit for heater 1 to 275C

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

; Tools
M563 P0 S"Default Hotend" 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 power saving
M911 S10 R11 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; Set voltage thresholds and actions to run on power loss

; Custom settings are not configured

homex.g:

; homex.g
; called to home the X axis
;
; generated by RepRapFirmware Configuration Tool v2 on Thu Feb 14 2019 01:42:50 GMT-0600 (Central Standard Time)
G91               ; relative positioning
G1 Z5 F6000 S2    ; lift Z relative to current position
G1 S1 X-308 F1800 ; move quickly to X axis endstop and stop there (first pass)
G1 X5 F6000       ; go back a few mm
G1 S1 X-308 F360  ; move slowly to X axis endstop once more (second pass)
G1 Z-5 F6000 S2   ; lower Z again
G90               ; absolute positioning

Does the wiring on the stepper motors look correct?

So I just booted my wired Duet Wifi 2 with custom configuration & when I try to home X or Y it raises one or the other of the dual Z motors.

I have a BLTouch wired sans the Duex expansion board as shown in the Wiki.

Anyone have any thoughts? I've confirmed the correct motors are plugged into the right positions. I've also disabled Heater3 in the config file for the BLTouch.

The wiring diagram for my stepper motors follow. I have them wired from left to right: Blue, Yellow, Red, Green