v2.2 CM should work right out of the box with Estlcam (no PROG pushbutton). I had some issues with the bootloader of my v2.2 board and I ended up reflashing the bootloader. I documented the reflash here:
I also used the standard Shapeoko configuration right out of the Estlcam box, and I don’t employ the Shapeoko homing switches (those I use with my GRBL controller).
Sounds like Estlcam contour mapping will get you where you want to be.