Besides measuring an exact dimension that would help JC give you the right door, also tell them what factory made your cab. Not sure they would know, but its worth a shot. Each factory could be off enough to have these fitment problems. Remember, its not just the door manufacturing between factories, its also the cab. If your cab is a Kansas City cab by chance, JC will likely have a door that fits because most of the yards we used to strip the doors were in Kansas and western Missouri.
The AD's weren't done in the 60's and beyond when tooling was so perfect that it didn't matter. These parts were made in an era when the tooling was done by hand and the stampings could easily be off by the amount you are talking about. Been there, done that. No matter what, think it through carefully. Since its on the frame and you are happy with the cab fit, sounds like its time for either another door or some modification.
You cant mess with the door very much because you have window fitment issues, stamped wraparounds, etc. After doing the mods on my cab, I have perfectly aligned and perfect seams and since I didn't mess with the doors, nor the inside cab dimensions, rubber and latching is also good.
You get people every now and then that cant imagine how tooling can be different from factory to factory so completely cant imagine how this issue can be possible. I have two AD's with this problem. The second one is because someone changed the door with 'just any' AD. A 53 that has one pull down latch and one pushbutton latch with the pull down side not closing at all just isn't acceptable! lol.
Too bad you cant take a trip to KC. Carter has entire outbuildings with doors everywhere. The internet sure doesn't solve everything. I know in my case life would have been SO much easier if I would have been willing to haul the cab to KC. But, all turned out really well anyway. Just added a month to the resto.