@dc42 I have been using this as reference. I was able to get the all of the axis moving in the right direction, but the probe is still not deploying before the z axis homing starts. I will keep digging further to see what I can find.
Here is my new config.g file, which is different than what I posted earlier and includes the changes made to fix the homing and axis movements.
; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool on Tue Oct 09 2018 16:04:57 GMT-0500 (Central Daylight Time)
; General preferences
G90 ; Send absolute coordinates...
M83 ; ...but relative extruder moves
M555 P1 ; Set firmware compatibility to look like RepRapFirmare
; Network
M550 PAIME FT-5 ; Set machine name
M551 PAIME1 ; Set password
M552 S1 ; Enable network
;*** Access point is configured manually via M587
M586 P0 S1 ; Enable HTTP
M586 P1 S0 ; Disable FTP
M586 P2 S0 ; Disable Telnet
; Drives
M569 P0 S0 ; Drive 0 goes backwards
M569 P1 S0 ; Drive 1 goes backwards
M569 P2 S0 ; Drive 2 goes backwards
M569 P3 S1 ; Drive 3 goes forwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X80 Y80 Z1600 E378.38 ; Set steps per mm
M566 X54000 Y36000 Z54000 E7200 ; Set maximum instantaneous speed changes (mm/min)
M203 X360000 Y72000 Z60000 E72000 ; Set maximum speeds (mm/min)
M201 X500 Y250 Z250 E250 ; 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 X300 Y300 Z400 S0 ; Set axis maxima
; Endstops
M574 X1 Y2 S0 ; Set active low endstops
; Z-Probe
M574 Z2 S2 ; Set endstops controlled by probe
M307 H3 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 P25 X-15 Y0 Z8.3 ; Set Z probe trigger value, offset and trigger height
M557 X20:280 Y20:280 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 C0 R4700 ; Set thermistor + ADC parameters for heater 0
M143 H0 S120 ; Set temperature limit for heater 0 to 120C
M305 P1 T100000 B4138 C0 R4700 ; Set thermistor + ADC parameters for heater 1
M143 H1 S280 ; Set temperature limit for heater 1 to 280C
; 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
; 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