Do you have a schematic diagram? You say you're new to EM repair, but what's your general level of repair and troubleshooting ability? The circuit for decrementing the ball count unit should be fairly easy to trace out with a schematic. Pinball Resource (pbresource.com) would likely have one for your game if you don't have one.
You say this happened after lifting the playfield, or do you mean it only does this only when the playfield is lifted?
A start would be to pull and reseat all the Jones plug connectors going to the motor board from the playfield, and the ones going to the light box (head). Do this with the game unplugged from the power source.