First thing you need to do is get the game straight into switch test mode when cold and watch what switch numbers the MPU board *thinks* are closed until it reports "0". These switch numbers will help pinpoint which switch strobe/return lines on the MPU board you need to concentrate diagnosis on.
Just make sure J2 is disconnected from the MPU board before you power on so no actual closed playfield switches invalidate this cold test.
BTW, is this a battery corroded MPU board? Can you post a picture of it?