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i use same config like you linuxcnc 2.5.x and an 3 axis mill (inkl tool changer )
I use Eagle 5.x with an ULP Autolevel program
Important is that your probe pin (google it in linuxcnc ) works
I use G38.2 Z-3 F25 for that
if that works you can use auto leveling.
I use it btw for 0 the z axis.
So i have an plastic vacuum table so i use the "needle" as one part and the copper of the pcb as 2nd part for the touch with the G38.2 command i find exact 0 of copper to "etch" it.
i hope that helped