Here's the code I used if anyone comes across this post in the future

M584 Y1 U2 P4 ;Separate Y Axis into Y&U and show U axis on UI
M564 S0 H0 ;Allow movement without homing as U axis not homed
G1 U2 ;Move right hand side of Y axis 2mm from endstop
M564 S1 H1 ;Enforce axis minimums and maximums and only allow movement after homing
M584 Y1:2 P3 ;Rejoin Y axis and hide U from UI

@jay_s_uk Thanks for this. I tagged it on the the end of my Y Homing and it works great.

@ian-0 Yes you should be getting a different reading.
For me I get a Probe status of 0 when it's not touching and 1000 when it hits the plate. If you are getting 1000 when it's in the air then you may need to invert the pin with a !

My z probe input is inverted and looks like

M558 K0 P8 C"!io8.in" H10 F120 T3000

and my G31 output is

Z probe 0: current reading 0, threshold 500, trigger height 10.000, offsets X0.0 Y0.0 U0.0

The thickness of the touch plate is dealt with during the probing sequence. I have a Macro that I run for Z probing which is a file called Z-Probe.g in the Macros directory, the code for which is below

; Z probe.g
; called to find workpiece Z via G38.2
;

var ProbeThickness = 9;
var CoordSystem	= 20;
 
; If the printer hasn't been homed, home it
if !move.axes[0].homed || !move.axes[1].homed || !move.axes[2].homed
	G28
 
; Display message without time-out and allow to position the bit
M291 T-1 S3 X1 Y1 Z1 P"Make sure the bit is positioned above the Z probe" R"Touch probe"

; With bit above center of probe
G91									; relative positioning
 
; Probe Z component
G38.2 Z{move.axes[2].userPosition - (var.ProbeThickness + 2.25)}	; seek until the probe circuit is closed
G0 Z5									; rapid move Z axis 5 mm
 
G10 P1 L{var.CoordSystem} Z{var.ProbeThickness + 5}			; store relative probe offset for coordinates system 1
 
G90									; Absolute positioning

Depending on your version of RRF, I don't think P4 is supported anymore.
Try P8 like below

M558 K0 P8 C"zprobe.in" H5 F500 T500

You might want to slow your probe speed down a bit as well but that's personal preference.

Here's the code I used if anyone comes across this post in the future

M584 Y1 U2 P4 ;Separate Y Axis into Y&U and show U axis on UI
M564 S0 H0 ;Allow movement without homing as U axis not homed
G1 U2 ;Move right hand side of Y axis 2mm from endstop
M564 S1 H1 ;Enforce axis minimums and maximums and only allow movement after homing
M584 Y1:2 P3 ;Rejoin Y axis and hide U from UI

@jay_s_uk Thanks for this. I tagged it on the the end of my Y Homing and it works great.

Hi,
I have a CNC that isn't cutting square which I think started when I switched to dual Y axis end stops.
I presume they are not quite level despite both being pushed to the front of the machine as far forward as they can be.
Is there a way to account for the offset in GCode or will I physically have to keep moving one of the endstops before I get it right?
I see there is an M666 command to adjust an endstops offset but this seems to be for Delta machines.