I am replacing the plates of my trim tabs with a larger size. The mounting holes for the new plates are in a different location than the originals, so I have some holes to fill. I'm thinking that I'll drill out the holes and insert a piece of dowel road coated in epoxy to fill. Anyone have any suggestions i.e. size of drill bit/dowel rod, etc?

I think those bolts are 1/2", so I would not really drill the holes out larger, just clean up the holes a little with the same size bit. I think I would use Marine Tex on the dowel rod and be sure to countersink the rod on both sides. Marine Tex the inside transom & use Gel Coat on the outside. Use no silicone to seal the dowell rod. I understand that Marine Tex is actually stronger when set than the 'glass it is bonded too. This would make a permanent repair.

I agree with BF.
Be sure to check compatibility of resins if you'r gelcoating the outside. Polyester gelcoat does not stick to epoxy.
Gary

These are Boat Leveler tabs, they're not through bolted. They attached with ~9 stainless screws. I think that they're 1" # 10 self tapping stainless screws.

The old holes will be hidden behind the hinge mounting flange so I'm not planning to re-gel. I've used marine tex before and will use it here.

like Gary said gel will not stick well to most epoxies, you could use a wood dowel with 3M vinylester filler[high strength repair filler] it is made for above and below the water line, and gel will stick, or you could use the repair stated above with white marine tex, it looks almost like white gel coat

A trick that I was told was to take a counter sink bit and you can counter sink it a little to help keep it from cracking back or shrinking.

Jon

run the countersink bit BACKWARDS to avoid cracking a chunk of gelcoat out.

I always pilot drill backwards thru gelcoat.

For example, if I'm going to use #10 self-tapping screws to hold something on, I'll take a 7/32 drill bit and run it backwards until I am thru the gel with it at the edges. Then I'll drill the thru hole in the normal direction. Keeps the spiderwebs from creeping out from under mounted hardware.

I've bonded in short lengths of soild fiberglass rod. Leave them low to the surface so you can add the Gel Coat to level it out.