Shop manuals usually tell you how to adjust body parts. It can literally include using a 2 X 4. Body gaps were never that good until well into the 80's or 90's. Usually they never came perfectly gapped from the factory. Get them as best you can with what little play there is and be good with it.
On a personal note, I would recommend keeping the flathead. I've ridden in cars that are stock and the same kind of car that has been hot-rodded. Night and day and I much prefer the feel and history of a car as it came from the factory but that is me. As for A/C, it has been done with the flatheads. With all windows down, the quarter windows turned to blow on you, and the cowl vent wide open, it actually gives a nice cooling effect.
We are spoiled now-a-days with A/C. The world ran just fine without it. Gotta admit I like it in my everyday driver though.