Quoted from RJPinball:Do I need to change out a chip on the MPU or something?
Yes, this is likely the case... and hopefully only one or two.
I did something like that once on my Gottlieb. I removed my slingshot scoring switch and left it hanging while I powered up, thereby allowing it to touch the high voltage solenoid power. The worst part is that it took me a really long time to correlate the new game failures with the root cause. Once I spotted the burn marks on the switch, I was able to trace the circuit back through the switch matrix and several chips on the MPU. Fortunately, I only blew out some gates on a 7400 and a 7432, and not the 6532. The two 74xx chips acted like fuses protecting my RIOT.