Pitted roof from rust under vinyl top repair

Looks like you have more than pits, do I see holes? I also see rust through in a section you posted that should require metal patching.
My process was to blast pits clean, rust converter sanded flush, epoxy primer/sealer, then high fill primer, then urethane base.

Overkill? maybe...
I`ll be going through this with my vinyl top cuda some day too. I don`t even look forward to that mess:(