Magooch's suggestion of making sure that your resins are compatible before starting.
Repairing holes I usually go overboard and put a layer of cloth on the underside then fill with a 2-part filler and finish off with gelcoat. Again going overboard on repairs I would use a stainless machine screw for attaching the new hardware and use a stainless fender washer and nylock nut on the underside. This should keep it from pulling out again. One final bit would be to trim the machine screw so that the end did not quite stick through the nylock. That way there would be no sharp edge to tear a float or dry bag.
The bow repair looks like a bit of reshaping with the 2-part marine putty and finishing with gelcoat. When we added rudders to our touring boats I used that method. At a later date the manufacturer saw our boats and we had a hard time convincing him that they weren't built that way at his facility.
Sea Kayaker Magazine