Did you resolder the pins on the fliptronics board? This could cause strange issues if they are dry jointed.
I would also replace the ribbon cables. They are 20 years old and get minute corrosion inside the plugs that is difficult to see. These cause corrupted data and you did mention you had scrambled DMD display initially as well?
Yes, get rid of those batteries ASAP as you don't want corrosion to sneak up on you and wreak the MPU board.
While on that subject it is NOT "acid" damage batteries cause but "alkaline" damage. They are alkaline batteries, this is the opposite of acid and it is the reason acid (vinegar) is used to neutralise the alkaline spewing from batteries.