The Ball In Play lights are controlled by a wiper (represented by the arrow below) on the Ball Count Unit.
Freedom Ball In Play lights (resized).jpg
It could be that the wiper and/or the contact board is dirty or the wiper doesn't have enough tension on the contact board. The Game Over relay switch won't be the problem unless you have trouble with the Player Up lights too.

/Mark

I'd guess it's in the back box but I don't know. Use the wire colors from the schematic and the fact that it only takes 5 steps and resets to the beginning as clues. If it's in the cabinet there will be a jones plug to go through but there won't be any other switches.