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Greetings,
I had the same problem, the door would not shut properly, and when I did slam it hard enough to shut "tight" it would vibrate, etc. Sometimes when driving I could look back (if not shut just right) and see daylight from around the door as it jostled.
My local mechanic said reinforcing the door (as it carries the spare tire) was required after checking some tech bulletins (which I have not been able to find) and trying to adjust the striker and where it connected with the door with no positive result. I just stopped in to check on the truck today (also changing the exhaust to 3") and the door was done.
Result? The door thuds now like the other four doors...huge change. What exactly was done to the door to reinforce it however, I do not know.