The holes don't show on all cars, I know they don't on vintage mustangs and tri5 chevys.

chevman wrote:The holes don't show on all cars, I know they don't on vintage mustangs and tri5 chevys.

Hard to see in an F body as well, You'd have to be looking for it, most Judges don't go that deep or are looking for such a modifications.

chevman wrote: So before installing the door for the last time, remove the pins on that upper hinge to body location, and replace them with only one 1/4" bolt. Tighten it finger tight, then just cut the head off, leaving some "stick out" past the installed hinge so it can be removed after installing the door. Then it will be easy to remove it and make the adjustment necessary on the heavier door.

Correction:
So before installing the door for the last time, remove only one pin on that upper hinge to body location, and replace it with a 1/4" bolt. Tighten it finger tight, then just cut the head off, leaving some "stick out" past the installed hinge so it can be removed after installing the door, then remove the other pin. That will maintain alignment without any slack between the lock plate and body.

The drop at the back of the door after installing the door glass, could be at the bottom hinge, or both, depending on the hinge/pin slop. The bottom hinge can be corrected with a shim. Just measure the gap at the front of the door to see which needs correction.