I presume the MPU board has suffered battery corrosion in the past?
Does the problem occur when both J2 (playfield switch harness) and J3 (cabinet switch harness) are disconnected from the MPU board? (you can disconnect them live).
If yes:
Switch the machine off
Leave both J2 and J3 connectors disconnected from the MPU board
Grab your multi-meter and connect the black meter lead to ground.
Set the multi-meter to measure resistance, if your meter is not auto-ranging, set it to 200k ohms
With the red meter lead, measure the resistance on pins 1 to 5 on MPU J2 pin header. They should all read around 56k ohms.
With the red meter lead, measure the resistance on pins 8 to 15 on MPU J2 pin header They should all read around 56k ohms.
Report back any substantially lower readings and post clear pictures of the MPU board.