Diode 17 on MPU board 1N4148 could be bad. The cmos chip 5101 itself could be flaky. Just to make sure you have 3 good AA batteries installed.

Possibly an intermittent coin door switch, the large white rectangle one.

Have you tried turning the game on/off quickly twice via the under cab switch?

Also assuming with all the work you've done, you have checked for any dry solder joints? Or even reflowed headers anyway?

This sounds like a 40 pin interconnect issue to me. Since you just replaced it I would double check your solder work, but I would also make sure when putting the two boards together that you give them a firm push to make sure the interconnect is good. From the picture it looks like you used the shorter pins for the interconnect, I think that's all that Big Daddy offers now, but I prefer to get the longer ones to make sure the connection is good.

Also make sure that your screws on the driver board aren't putting too much pressure in the middle and making the interconnect actively worse.

Only a few times with the diode and many with bad/flaky cmos 5101