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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.