[Dalaigh]

Without the fender there you have nothing to adjust or line the door to. I've put many doors on these trucks and have never taken the fenders off, unless I've had to replace them. Tape up the edges, and get a buddy to help, you need help anyway the doors are awkward to do by yourself (unless you have a door dolly).

To the OP...
It sounds like it is your pins and bushings, but check your hinges as well. They may have slipped, It happened on one of my old trucks. The previous owner didn't tighten the bolts enough when he put new doors on the truck.