Success! After restarting the printer, I was also getting errors "G90: Probe was not triggered during probing move" after it finished its homing moves. I looked in homeall.z and it ended in a G90. That really shouldn't have impacted it so I commented it out and ran it again. This time, no errors. To test it again, I removed the ; to comment it out and it still ran fine. No errors. Go figure. I am now able to get it to home properly, do a 4 motor gantry level and run mesh compensation. Mesh compensation takes forever now because it probes the bed twice at each point and, over a 400mm square bed, that takes a lot of time. I'll tweak its settings.
Thanks all for the help. This forum is one of the best out there for solving issues.