Yep! check wiring and connectors indeed....
Only other thing that's sprung to mind besides an open ground or signal wire from the door, that could cause a hang at the adjust menu, is power supply rails to chips dropping off as circuits boot and draw more, so failing loom/connector issues I'd check the legs and sockets of anything transferred are making clean contact despite how they look.... just in case, but MR Maniac is right, they're pretty fussy and usually it wouldn't get that far.
the backup battery difference bugs me. A pic of both boards would be ideal.

nv ram version you have there... no batteries required... should also have come with full schematics?
one connector has less pins but aside all should be in same place.
bad connection issue still?
no chance you had play field up and knocked/bent any switches in trough area?

quote "connector CN3 on new MPU only has 9 pins while your game’s connector may have up to 12 pins. extra pins (10-12) on your game’s connector are not used. Install the connector housing so that the key at pin 6 matches the cut key.... just a thought... haven't gotten as far as CN3 on schematics yet

also double check dip switches DS1, incorrect setting for game can cause certain solenoids to not work... trying to find where I filed the settings....

flippers and bumpers working? that's a sign if not.

cant find em but I think its 1-4 towards blank LED, 5-8 upwards ditrection..... take photo of how they are first, Ive made that mistake before...

DS1 looks fine to me , If that's how it was then were going elsewhere.... think Maniac is onto something with a missing power rail....

try this... If two game PROM chips are used at position 5B and 5C, jumper J4 must be installed and jumper J5 must be removed.
If a single game PROM chip is used at position 5C, jumper J5 must be installed and jumper J4 must be removed.
Remove jumpers J5B and J6B at location D8.
Install jumpers J5A and J6A at B7 and D7.
Add 3 pins to CN3 (top-right of board).
Remove the EPROM from the socket at position B5 (if any).

ignore the 3 pins on CN3 as thats display related.... try those one at a time, reverting any ineffective changes before proceeding. there may be discrepancies between rev2 and 3 of the mpu so some stuff may be wrong in that list. basically its doing a ball search when it shouldn't be so wont initialise a game. I recon one of those jumpers is incorrect or there's a voltage missing somewhere.
not ruling out a faulty mpu of course but I know you don't want to think about that

this should clarify...

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so my previous settings were off a bit

nothing wrong with any trough rollover switches etc? could be fluke simultaneous issue and common on those, I'm sure Iv'e had this same issue with a GnR machine, same exact setup, just cant remember what it was!

Id go into diagnostic mode and start testing switches and solenoids in that area, might see a pattern or group that play up leading to the culprit

check Q54 it may be fried, it runs the trough, also all coil diodes in that circuit, they usually cause it to go.
good night, hope you have better luck with her in the morning....