I just recently wrote some code to do pcb milling with pretty close tolerances. The actual milling table wasn't straight however, so when the substrate was clam

I just recently wrote some code to do pcb milling with pretty close tolerances. The actual milling table wasn't straight however, so when the substrate was clamped down it would have Z variations 3x larger than the desired cutting depth. A 5 minute touch probe run and a simple 2D compensation table removed the need for a time consuming tramming operations and expensive clamping hardware. This wasn't so much fixing as augmenting. Software has the unique benefit that it can replicated essentially free while the physical improvements need to be administered separately in each and every instance. Re. the backwards wired motors. Storing a config table in EEPROM seems to be a simple and portable solution to this. Do it in the logical way until you hit the output pins.