Greybeard:
Can you post s few pictures of this project? The body on the frame, and the body mounts would be helpfull.. If you can't get a pic of the mounts, if you can somehow put arrows in the pic..."Mount here" or something.
When the body was off the frame how was it supported?.. And are you sure the new mounts are on the same plane as the old frame? It doesn't take much to twist a body out of shape. Probably a matter of tweaking the mounting points. I'd be real skeptical about using an inch of shims to square up a door if it didn't need it before you took the body off.

Sincerely:
Paul...aka xerxes