Game was working fine. I turned it on the next day and it blew fuse 6F3 repeatedly. I found a post here that mentioned it might be the large diodes on the power supply at D7 and D8. I had already recapped the power supply board but hadn't changed the diodes. I replaced the diodes and the game was back up and running.

A friend came over and we played for 2.5 hours with no issues. I then unplugged the remote battery holder for about 5 minutes to reset the game to factory settings. When I plugged the batteries back in and turned the game on it wouldn't exit audit mode. I tried setting it back to free play (setting 18 value 00) but it wouldn't display 00, as if the memory was corrupted.

I removed the MPU/driver boards and socketed in a new 5101. When I plugged everything back in it started blowing 6F3 again. It's blowing the fuse when 2J8 on the driver board and/or 1J2 on the MPU are plugged in.

Any help with next steps would be appreciated!

Got it! A previous owner had used the wrong screws to secure the boards to the brackets. Turns out the screw in the upper left corner of the MPU board had a head large enough to short the ground plane and the 5v line.

I found it by unplugging all cables to the MPU/driver boards and still had a short between test points tp9 and tp10.
I then removed the pair of boards from the game and tested again while they layed on the playfield glass, no short this time.

I put them back into the game and was able to get the short to clear when the screws weren't tight.
I put test leads on tp9 and tp10 and tightned the screws one by one. Tightening the upper left caused the short to reappear.

A visual check showed the screw head had removed some of the green masking on the trace below the ground plane so the screw was shorting it to the ground plane when tight.
Sure enough, that was it. I used a smaller (the correct size) screw on that corner and she boots up and plays fine now.

Most of the rest of the holes are now reamed out too much for the proper screws to thread in. There was one more corner that had a trace near the ground plane - driver board upper right if I remember correctly. I happened to have one more of the correct size screw left, so I put one in that corner as well. The rest of the holes don't have traces near the ground plane.

To fix it 'properly' I'd have to buy replacement brackets and screws so they're all correct. I'll worry about that later.