All I can give is the jackass answer of change the hinges and latches and either shorten your door or build a recess into the body for the door to shut into.
I believe you unrivet the cowl from the subrails and move the cowl forward. Once you have the door fit flush you move the body around to make up the differance if you are running a stock length hood. Friend did it on a 30-31 Roadster, not sure I'd spend all that time.
I did it once on a pickup I built. To do it right is a ton of work half way in I wished I never started. I started by moving the back of the cab back. This got them flush except for a little edge trim at the bottom back edge of the doors. Then I built door jams with new style latches . One of the hardest parts was making latches work in the thin doors (the glass is in the way).
I moved the rear of the body back on my first Model A Tudor. The floor and roof both needed to be redone, so it wasnt a big deal. I didn't like it after I got done lining everything up and tacking the subrails and roof together...so I put it back to the stock location. Flush doors just don't look right on a Model A.
This isnt going to help any..but i like the look of the doors on Model A's ..especially the early ones
I didnt move anything back. I simply marked where the door overlaps and cut a corner out of the body creating an area for the door to fit in. Then I welded an angle that was shrunk and streached the contour of the body into the cutout. I made it deep enough to put some weatherstriping in to finish it like it was done by Henry back in the day. Lots of work but well worth it!!! Saves on the paint chips!!!!!
Personally, I think it is more work and expense than it is worth. When the model a door is adjusted and fits correctly it looks just as good as flush fit doors. http://www.jalopyjournal.com/forum/showthread.php?t=409232