My first Mopar/Questions?

So I'm picking up my first project car Sunday, which happens to be a 1971 Scamp. I'm super excited and anxious to get started on her. The car has already been taken apart and ready to start bodywork and painting. So now for my question. The car had a vinyl top and with that came plenty of rust underneath. I have only seen one hole which happens to be right in the center where the windshield meets the vinyl. It's a pretty good size hole and I can post some pictures of it when I get it all home. What is a good way to remedy this problem? I do not want to go back with a vinyl top and I don't want to really half *** it and make more problems for my self down the road. I'm decent with fiberglass but I don't think that's the right route. Any advice would be greatly appreciated. I'm sure there are prob more spots that need repaired on the roof, just haven't seen them yet. With the exception of the passenger side floor board and roof the car is rust free.

EDIT Pictures: