hmmmmmmmm.
Is the ground braid attached in the head? https://pinwiki.com/wiki/index.php?title=Bally/Stern#Inspect_Harness_Wiring
Is the polarization correct on the coil diodes? .... https://pinwiki.com/wiki/index.php?title=General#Testing_the_coil_diode
Are ALL the connectors on the boards "keyed" and installed correctly? https://pinwiki.com/wiki/index.php?title=Bally/Stern#The_Importance_of_Keying_Plugs
Is there corrosion on the MPU (sadly quite common) https://pinwiki.com/wiki/index.php?title=Bally/Stern#Repairing_Alkaline_Damage
Post some pics of the boards in the head