I have a '59 panel and had the same problem. After inventing a total of 16 new cuss words trying to get my doors to line up with each other as well as the body I figured out the secret. The key is to align each door with the body first. Next, either add or subtract shims where the bed floor is bolted to the cross frames at the rear and next to the rear set of bolts. This will actually create a twist which will line the doors up perfectly with each other. It turned out to be so simple that I'm sure thats how the factory probably did it on the line.

DDAUTOPARTS