I'd fill flush with marine-tex or other epoxy, like thickened Raka or West Systems. If it were mine, I'd even drip some thin penetrating epoxy into the holes if blind holes first and add the other when this kicks. If a thru hole, you can still wet with thin epoxy, but you need a syringe.
Lastly, after filling close to the top, you could add countersink bevel to the hole first and then this will give enough raw glass for gelcoat to stick too.
You're close enough to me, maybe 1.5 hours away, we could always meet up in the KTP parking lot in Kittery and knock it out in less than an hour ... less the final gelcoat topcoat, which is easy.
