The factory did not paint the roof of vinyl top cars. In addition, the holes drilled for the trim, and the installation of the clipd on the rivets all had the chance to cut through the paint. Hence the rust. If you want to "prep it properly" you should just prep and paint the roof. you don;t have to worry about making it perfect, just get material everywhere. Then install the new top. Personally I like them, and if a car had it, I'd put it back that way.
