This might help narrow down the new flashing issue:
Flicker: MPU reset good, program booted.
1st Flash: ROM Checksums OK
2nd Flash: U7 6810 ram OK
3rd Flash: U8 5101 ram OK (U8 & U13 on mpu-200)
4th Flash: U10 PIA OK (see details for caveats)
5th Flash: U11 PIA OK (see details for caveats)
6th Flash: U12 555 Display interrupt timer OK
7th Flash: Zero crossing interrupt detector OK (solenoid voltage present)

http://pinwiki.com/wiki/index.php?title=Bally/Stern#Bally_.2F_Stern_MPU_Board_LED_Flash_Sequence

Hell at this point reseat all the connectors on the rectifier board. J1 J2 and J3

But when you have all the connectors unplugged clean the pins the best you can with an eraser. You may need to reflow some solder on that board.

This thing was fine, you left it on a while now its acting up. Probably heat moving things around cracking old solder.

Any progress?

Great news, glad its back to life!