The only other obvious place I'd look is the leaf switch on the flipper button itself. I'm only saying this because I know from experience with my JP that they can loosen and slide to the left/right so that there's no contact just for the top flipper, and once I dropped my playfield by accident and something hit the outer leaf swtich and screwed up just the top flipper.
Good luck with it. Frank is a favorite at my house.