I have been rebedding the deck hardware on Shanti, my 1977 O'Day 27 as part of a major overhaul. Sounds like you are on the right path – over size holes, epoxy, rebore... I would add the following; when possible countersink - just slightly - the underside of the hardware even metal fittings can be countersunk. Teak or other wood fittings are easy of course. I also countersink the top of the deck just slightly into the fiberglass. This creates a small reservoir for the bedding material to sit in. It prevents total squeeze out and provides a thicker gasket right where you want it. I have been using Boat life caulk with success. Pay attention to the materials you are bonding not everything is compatible. Also remember you do not want to compromise the structural integrity of the deck or fittings.
I find child labor often to be very helpful …even when it is involuntary...