Carefully check that the ramp entry isn't cracked on the left hand side. Early upper flipper shots can slam right into this side and although there is a metal protector, on mine it wasn't enough and it's cracked. Mine had water damage from condensation around the edges of the translite so although not specific to JP I'd look closely for that.
Also, relating to the t-rex advice above, test it during gameplay with the glass off but note that he only eats the ball the first and fourth times (when completing T-REX) so don't freak when he doesn't eat on the second and third times
Check the Control Room scoop by throwing the ball in there. Do it lots. If at any stage it doesn't register then you may need to replace that switch — it tends to get hammered because it's the most used shot in the game.