A few things to check
Check fuses with a DMM (not just eyeball)
Reflow solder to all header pins on all boards
The 40 pin interconnect between the MPU and the SDB is almost always suspect. You'll need to replace the pins, both male and female if not done already. I've read that some people say that there's no point in further troubleshooting until this is done.
I would start there.
Also this thread
https://pinside.com/pinball/forum/topic/vids-guide-to-bulletproofing-williams-system-6