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777: You are likely to get a number of replies because many Whaler owners have been down this same route. The root cause appears to be that the deck above the fuel tank is not made as waterproof as the rest of the boat. The flimsy mat used to seal the core plywood cracks around the margins (and sometimes in the middle, near access covers) and water finds its way into the core. As Pinion mentions, sometime it looks good because you can't see it behind the fiberglass covering. The "best" solution is to pull the deck when you have time and check from the bottom side completely. If it is ok, then you can fix the bad areas and put it back with some piece of mind. If it is bad in many places, you can easily strip off the plywood, and replace it doing a proper job of making it waterproof. There are many repair videos and/or photos of this repair on this site and other places, so I am not going to attempt to describe it. Let's just say that it is not a difficult job, just dirty and you must proceed carefully. If you are not handy with wood and fiberglass (epoxy too), you could farm this out to a professional.

With regard to your proposed repairs, it is hard to visualize without some pictures. Best way to get good advice is to take some pics and post somewhere members can access it. However if the backing wood, into which the deck screws are installed, is wet, you probably should let it dry after you drill it out. Wet wood will not hold epoxy or polyester resin. What you want is for good, dry wood to absorb the resin and form a strong "hockey puck" into which you can drill and remount the screws. If you drill into black wood, meaning it is rotting, then the repair can grow in scope. Again, I am not going to describe what to do in this case, as there is lots of advice. And many people have different valid ways of making the repair. For example, some people would use thickened WEST system epoxy, some MarineTex, some mix their own by using chopped fibers and resin.

Putting Gluvit (which is epoxy resin) into the holes to strengthen the wood is fine, but only if the wood is dry and in good condition.

Also you ask about putting MarineTex into a caulking gun like the WEST system. I don't believe this will work because MarineTex is extremely thick and viscous, where injection of other resin mixtures is thinner and will flow much better.

Take your time to research the alternatives. As Pinion wrote, you might be better off pulling the deck after the season and doing a good inspection....especially if you like the boat and want to keep it!

Al