never seen a shim on a door hinge and i have a collection of 2 half doors and 2 full doors, got any pics? besides a shim behind the hinge would push that front part of the door into the jeep and push the rear away from the latch, that is not the problem, the front to rear dimension is the problem, and it is because the edges of the seal have not been properly warn out/smashed close enough to the door itself.
i also have replaced my windshield cowl SEAL. and it came from the factory too fat to EASILY pull the windshield tight enough to the roll bars. A guy from work pulled on the windshield towards the rear, while i bolted it up! it comes FAT because they want it to wear in and seal properly (i am assuming). the Same is for the seals for the doors, the will shrink/SMASH themselves smaller, i can tell a difference in 1 day already. where it catches at the moment, is right at the latch, the rubber is just a little too big and it hits the tub before the latch clicks. I am just looking for a process to speed up the "shrinkage". IE: torch to warm it up then hammer on it to try to get it to tighten up to the door right there at the bulky location. now when i typed it out just now, that did not sound like a good idea, so..... i may wait a week and see how it goes.
the 2 bulky parts of the seals have what feels like metal wires in them to help keep the proper shape on the door corners (so they are somewhat malleable.