I have some premix short strand fiberglass filler (dark green) for the initial filling.
That's the stuff to use, although you might consider making some yourself because the dark green will be hard to hide with white gel coat.
I'd lay a layer or two of glass tape on the inside of the hole to reinforce it.
Then just take some resin and mix in some chopped up fiberglass until it's thick and spread it over the deeper spots to build them up. Trim it while it's still "green" (not fully hardened). Fair out the surface with a fairing compound (like Formula 27 or Bondo - remember, white or light gray is easier to hide).
Spray with white gel, wet sand and polish and you're as good as new.
Put a foot stap over the part behind the rear crossbar and you don't have to worry about re-creating the non-skid.