Are you booting the MPU in the game or at a lab bench? Maybe take off all but J4 to see if that impacts how the MPU is booting up? Are you sure the replacement 5101 chip is good? I like NVRAM in these cases as it rules out one possible issue.

Check for shorts by the IC sockets. I once had a very small solder short across two traces under a socket. I couldn't see it and found it doing continuity checks.

Was the MPU like this when you got or was it working and then broke? As usual, check all of the previous work very well. Have you tried new ROM eproms?

Hard to believe, but 1994 was 25 years ago and a lot can change in that amount of time. I should have asked the obvious - how is the battery acid damage? I've seen all sorts of weird behavior due to acid damage in weird ways, such as causing a via to go open.

The U6 EEPROM has a partially exposed window where the sticker pulled back. Maybe the ROM is corrupted?