I'm not one of the great repair techs here but I figure I'd give a shot at helping. Try removing the fuse to the backbox GI to isolate that out and see if the flickering problem still occurs. Also, when the GI flickers do you hear a relay clicking or does it simply flicker? I ask as I believe there's a relay that flickers the GI when a certain event happens during the game.

The next part will require time and patience but I would trace your GI lighting wire from the power supply to the end of the last lamp just to make sure nothing is touching that shouldn't. You'd be surprised how many off things you can catch from a visual inspection.

Given what's happening though I feel as though there is something going on between the end of stroke circuit of the flippers and the GI since the flickering occurs when pressing any flipper. Since I believe the GI is separated from the general circuitry of the board I don't think it's an IC or anything like that though I could be wrong.