I don't understand what booting to zeros means?

So your mpu boots fine, flicker of LED then 7 flashes of the LED?

Have you tried a switch test via the front door?

Reseat both left MPU connectors and both Right driver board connectors. If there is any improvement at all, I would change these 4 header connectors on the boards and repin these 4 wired connectors.

so in attract mode do the zero's go off then back on with the high score to date?

or it doesn't go into attract mode?

maybe the audit switch is faulty?

guessing you have checked all the soldering of the header pins on all boards and reseated all the connectors, checked fuses and test point voltages?

The DIP switches on the MPU board are part of the overall games "switch matrix".
MPU DIP switch 31 shares a signal with playfield switches.
MPU J2 is the switch harness connector to the playfield.
So if disconnecting J2 resolves the problem of the game booting to 000000 audit mode, then you have a short circuit on that signal somewhere on the playfield which as a side effect causes game to think DIP switch 31 is ON - hence the player audit boot mode.
Did this problem occur straight after you were playing around under the playfield?

The DIP switch 31 signal is shared on J2 at pin 14, it's a brown-white wire that runs to the playfield and connects to the following switches:
1) Weighted tilt switch near the flipper mechs.
2) Left outlane switch
3) Middle zero "0" standup target switch
4) Right pop bumper switch

Very carefully inspect these switches for an accidental short to something that shouldn't be.