The MPU board 6821 PIA chips can be determined as "faulty" during the power on self test if one of their port A pins are shorted to ground or something else.
U10 port A controls the switch matrix, lamp board and display numbers.
U11 port A controls the display digits.
All the lamp and display signals go through MPU J1.
If by chance when you were diagnosing your 12 volt issue did you disconnect J4 from the lamp driver board and accidentally reinstall it off by one pin or upside down?
The only way I can see J1 and/or J3 from the lamp driver board to cause this issue is if there's a shorted lamp socket to a switch on the playfield - but even that's a bit dubious.
Quoted from QuietEarp:What could this mean? Repin board and connectors J1 and J3?
Don't reterminate your connectors for this issue. The error condition was a short circuit, not open circuit.