lodown-
This may not be a major problem and possibly can be fixed in seconds. In many cases Ford used off-set dovetails to align the doors with body accent lines. This was done during production. A case in point is my '35 coupe. The body has never been separated from the frame nor has it undergone major body damaged. Both doors align perfectly with the body and close like a refrigerator. Here is the important part, it has factory installed off-set dovetails. If you remove the dovetails and replaced them with the normal, garden-variety type of dovetails, the doors will no longer align. If you get a chance check Ford's "Automotive Hardware and Trimming Supplies" book it shows pictures and part numbers for off-set dovetails. Now the "bad" news. To the best of my knowledge, no one is reproducing these off-set dovetails so, you may need to be creative.
At any rate, I would definitely begin by changing the dovetails before I would start pulling things apart and start shimming the body.
Tom