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At a guess you have closed-loop control of the spindle, but the PID is being commanded by absolute spindle speed request.

I am not sure why you used Stepconf at all. You should have been able to just copy the old "linuxcnc" directory from one drive to the other, and carry on as before.

M3 probably _could_ be remappable. It would just need the hooks adding to the code. After literally seconds of contemplation I can't think of anything that means it fundamentally couldn't be remapped if the code was modified to handle it.

The issue is that I'm not even able to move the robot arm, because it requires me to perform a 'Home All' operation before initiating any movement. I'm 90% sure that the problem lies in the incorrect application of DH parameters on my part. The tricky part is that it's so simple, I have no further idea what could be going wrong. I've been stuck at this point for a couple of days now, and still no progress. Later, I plan to rebuild the project from scratch to avoid any unnecessary correlations with the original Puma source files. Maybe that will help.