Lenny, to begin with, Ford assembly workers did not use ‘shims’ originally. They were not needed as the body blocks and the single woven pad were of the correct thickness and the doors were properly aligned when the body was put together. In the modern era of ‘restoration’, often times shims are used as a way to try to compensate for a component/components that were not restored to factory specifications originally. So as Bill is saying, a bent frame, incorrectly sized body blocks, bent door hinges, incorrect thickness cowl anti-squeak, reproduction hood, etc., etc. can be the culprit. Generally speaking, having someone who is knowledgeable and versed on aligning sheetmetal on these cars is the best way as it can be very timely for someone who is inexperienced in that area. Do you have an experienced restorer in your area that can assist you??
Based on a quick guess, my thoughts are worn or damaged door hinges first, followed by a damaged frame?