Poor Panel Fittment
I know this isn't what you want to hear but Russ is right ~ this series of GM trucks were made during a time of accute shortages , every single one was sold right away as these were the first all new trucks after WWII and of course , the best you could buy anywhere so GM only ran two shifts and shoved them out the door absolutely as fast as they could .
The poor jigs on the basic body assembly , were legendary .
Passenger side door fittment and water leaks , terrible wind whistles plauged these trucks when they were new , 50 + years of hard work hasn't helped .
To address your problem , you'll nee to repair ALL cab rust and the under floor supports then correct any frame twists (most of these had bent frames when new) and replace all the rotted away cab mounts , rebuild or replace the hinges then (and ONLY then) you can remove the door's outer skin and shim and adjust it until it closes correctly and then dress the fitment of the outer doorskin before re welding it into place .
Or , if it closes now without slamming the bejeebers out of it , just leave well enough alone .
Sorry to give you ths bad news but that's the facts , Jack .
John-John in my Shop , has spent years screwing around with the passenger side door on his '49 3100 , it's really close now but still not perfect , this on a Hot Rod built by a Professional Builder whos way too picky IMO .
YMMV , IMO and so on .
Best of luck with it .
Whatever Russ or Evan says about Body Works , take to the bank .