I would wager that every door is just a bit different, so a door that fits good on one truck may not be a good fit on another.
You may have to get a jacking bar in the door frame and do some adjustment. Your opening may be squashed a bit (as in the top of the door frame is pushed backward or forward.) The A pillar above the upper hinge could be misaligned and pulling the top of the door opening forward enough to cause a rub with the top of the door at the rear, even though the molding lines up.
Some guys have ground the edge off the door and welded and ground the weld to get the proper gap.
You might have to resort to what a body man did to the family's 54 Chevy Station wagon in repairing it after a t-bone by a drunk. The two right side doors got replaced, and when my Dad picked it up, he noticed that the rear door wasn't properly lined up. The guy took a pipe wrench from my dad's shop truck, stuck it in the lower hinge and slammed the door shut. It fit just fine after that.
Measure your openings at various points both right and left (largest diagonal measurement in both directions, lower hinge mount to top and bottom rear, latch mount to top and bottom front, etc.) and compare the measurements side to side. That may point you at where the problem lies.
