The hinge bolts on the door have some play. I would try loosening the bolts and adjusting the door position. You might get the door to close flush with the cladding that way. Also, I remember the very bottom of the door is just a cladding lip and can easily be bent straight.
Do you have any pics? I worked extensively with a damaged door when I built the spare tire carrier. The body work wasn't too difficult but it's hard to give advice without pics.