A Lot of questions: See how I do with the answers.
1. Replacement Screws. With the exception of the vary largest bolts, everything is available in stainless from WEST, except that they will have Phillips heads. The largest bolts, like the ones that hold the coaming to the cockpit, are available from Jamestown Distributors, as I recall. Only use either stainless, or chrome plated brass (No cadmium or zinc plated steel because of eventual rust).
2. What I have used successfully for filling the holes, when the wood screws don't hold, are slivers of wood forced into the empty screw hole. The best choice, in my opinion, are slivers shaved from hardwood furniture pegs. Mahogany slivers are OK, as are wooden match sticks, but the mahogany is softer. Just shove them down there until the hole is full of the sticks, break off the slivers flush with the surface and then put the screw in. If the screw is load bearing, then fill the hold with some sort of water repellant glue, like Franklin Hide Glue, before pushing the slivers in and . Then pur the screws in and let it dry.
3. The clear substance might have been a silicone sealer. However, rather than using that, I would recommend, and have used a sulfite, like 3M 101 for the purpose. Do NOT use a polyurethane adhesive (like 3M 5200). You need a sealer, not an adhesive so that you can get them off if you need to at some time in the future. Don't use the silicone again because if any of it slops over on the fiberglass, paint will not stick, even if you wipe the goo off.
Best wishes on your endeavor. You have a super boat.