This is why I always tell people to try to stick as close as possible to same year on door swaps. The stamping dies for sheetmetal wears over time, so as the years go on, the pieces will not be the exact same shape as they were the year prior. I could probably also go so far as to look at the plant the truck was built at (can be easily decoded from the VIN), but I don't honestly know if each plant had their own stampings or they just shipped them in.
Honestly don't know how you could fix that, homie, short of removing the hinges which are welded in place, and installing replacement hinges which bolt in - and then being able to adjust their position. An expensive and labor-intensive proposition to be sure.
I started mentioning the year thing a long time ago when I ran into the same exact problem. The fit issue was different, but apparently insurmountable. Door fit fine at one end but was waaaaaaaaay off at the other.
Solution? I'd hunt for another door.
Richard