So the machine is worse than I was hoping. Not sure what is wrong, but it's seems fairly serious. The RPM sensor was acting up again, and I think I know, which connector it is now. The Z axis is still acting up a little though it is better than it had been. On occasion when a move is commanded it will delay then lurch into motion. I'm starting to suspect the commands may not be reaching the servo driver.
So I was just running some test to see if it was better or worse today since the machine will work better after a day of working on it. I cleaned some of the screen connectors hoping that might help the line issue (it didn't). I tested the tool changer, and it worked a couple times. Then I noticed that sometimes when the shot pin engages to line the spindle up for the tool change it will stop the spindle early. I'm already running the spindle a little faster than it is supposed to be for line up because the motor is weak moving that slow. So, I want to use a little sand paper to polish that part of the spindle because it was rough from the shot pin. I was running the spindle slow to oil it after polishing it when the machine went ballistic. It blew up the shot pin engaged sensor (using the shot pin as far as I can tell) ran the tool changer arm all the way back. The only buttons I pressed were spindle on and start so only the spindle should have come on like the last 2-3 time I had turned it on. I had done this or similar much milder a couple time before, and I just thought it was a loose connection to a button or something activating other systems. I'm starting to suspect that I may have a problem with one or more of my control boards. I will be pulling them tomorrow to see if I can see the problem and check them over.