For all of these games you must address certain things. Every single Sys 3 - Sys 7 game needs these things done or they will not be reliable.
Replace the 40 pin interconnect between the MPU and Driver board. Replace the female side and resolder the male pins. This is Mandatory before you can accurately diagnose the rest of your issues.
If your MPU has any acid damage on it from the battery, you must neutralize it and then repair/replace the affected components. Usually this will mean the 5101 in a new socket at a minimum.
Next you need to make sure you have the proper power at your power supply board going to the rest of the game. You can refer to the manual and verify with your DMM each voltage at each Test Point.
After this you need to assess the health of your connectors. The IDC connectors used in this series of games are junk and at minimum I replace the connectors for the Switch Matrix, Switch Row, both sides of the MPU to Sound Board interface, and the Special solenoids/Flipper connector. While your driver board is out of the game make sure to check the header pins for cold solder joints and resolder where necessary.
Complete all of these and if you still have issues we can take it from there.
PS> Don't waste money on an "overhaul kit". Buy the parts you need from Pinball Life, Marco, Little Shop of Games, Planetary Pinball/BAA or the other great vendors. Gorgar only uses one ball by the way. The smaller ball is used in the roll tilt mechanism inside the cabinet on the left.