Gameplan MPU's suck hardcore when it comes to repairing them. Tripley so if they have battery corrosion.
What game eproms are in the MPU's? Are they all Sharpshooter 2 roms or are you swapping the roms from a 4th known working board that came with the fully working game?
Gameplan heavily recycled the game software/rules from title to title but they aren't identical AFAIK.
Are the boards strapped correctly for the ROM sets you are using? Never found a good source that correctly identifies what to do and these boards are notoriously fickle that I was always afraid of messing with ROM jumpers on these turds.
Also FYI in case you don't know. The boot up sequence sounds like it works like the Bally boot sequence but it doesn't.
i.e the stuff needed for the game to get to the second flash includes the stuff tested at later flashes. So if the parts for flash #5 aren't working you won't get flash number 2. I think there is maybe one flash (the 6th IIRC) that you can get to that accurately states that that part is wrong. Otherwise you get no flashes or ALL flashes and pretty much nothing in between. Worthless.
Turn off the dip switches and run the switch tests with the pf switches disconnected from the board and use a jumper wire to test the switch columns and rows. I had a bally with switch issues once and it had a couple of bad diodes on the dip switch banks.
Good Luck
I fixed a shit ton of these about 10 years ago. Got around 10 out of 20 working. Kept 2 spares on a shelf. They didn't last a year sitting. Pulled them to use and both had died. Awful systems. The batteries usually manage to wipe out around 12-17 chips and their traces.