This is from Vince Falter's site on a 1930 coupe. It would be similar for any model A coupe body. If the rivets that hold the quarter panel to the sub frame are still there, ie not completely rusted away, then they would need to be drilled out but there aren't all that many. They are just in key locations for structural strength. The crimp of the quarter under the edge of the sub rail is another place they like to rust away. I'm not sure if it was spot welded or not but spot welds can also be drilled out. Connections at the belt rail and cab should be spot welded too unless they used bolts.
http://www.fordgarage.com/pages/quartersbefore.htm
I would make sure the frame is straight and rework it to be as straight as possible since it will be the basis or foundation for the sub rails and floor. Add the quarters and square everything for best fit before riveting or structurally attaching anything. When everything fits well, you can nail it all down for keeps.
The sport coupe to standard coupe conversion would be a job since the quarters are different stampings. Welding a top on there will require a lot of fitting before the cab top is attached. I think I'd just trade it for what I wanted rather than convert it. It would be a lot easier to put a sport coupe or business coupe top on it than to go the standard coupe route.