I would use polyester resin, thickened and colored, to fill the holes. I've been told by the pros that polyester doesn't like to stick to epoxy. After filling the holes I would do as Todd suggests, apply the finish gel-coat with a chip brush, then sand it flush with progressively finer grits finishing with a 400 or 600 grit wet sanding then buffing with rubbing compound if you want a shiny finish. There is (was?) an outfit in MA that would match gel-coat if you could provide them with a sample. Mike Casey in Freeport can help you with contacting them and any supplies you might need.