Pitted roof from rust under vinyl top repair

For rust pits on a vinyl top car's roof and prepare for a new vinyl top, at first Remove the existing top, clean rust, apply rust converter, fill pits with metal filler, sand and smooth the surface, apply epoxy primer, install the new vinyl top, use sealant to prevent water infiltration, and optionally, use lead filler for seamless edges.
For Epoxy Primer Over Etch Primer this article is very informative and helpfull-
Epoxy Primer Over Etch Primer: Will It Work Well?