Something to understand about those GM cars is that GM built as many as they could as fast as they could and as cheap as they could. So when we try and make one perfect things don't fit like we want. the fully assemble with drill screws is an excellent idea in my world. Then you can see just what needs to be fixed or modified to get the fit you want. i would start with the doors and rockers so the doors fit right and work from there.
Bracing the body with a temp framework made from light square tube will be a big help as those things can get floppy when sheet metal is removed for any reason..
I would recommend you get this DVD as it is about the best I have seen on metal working. I have a copy and refer to it often.