I had noticed a little bit of a separation where the skeg trunk comes into the hull, so I dabbed a bit of epoxy on it, and continued to use the kayak.
I noticed that the gap had increased somewhat, so I brought the boat downstairs to take a look.
WOW. When I pried at the gap, I could see that the damage was extensive. It seemed that I peeled away water-soaked plywood until only a skin of veneer, and the fiberglass on the outside remained.
I wondered if it was worth it, if I should just take the box out somehow, and do without. I can barely reach it through the aft hatch, let alone work effectively with a heat gun at arm's length. A lot of work went into the thing, plus the potential of an ugly "plug" leaking itself, so I'm going to try to fix it.
I dug away seemingly endless shreds of moist wood, until I couldn't get any more out, and hit it with a hair dryer until it stopped smelling "wet". I cut a piece of 10 oz, and a piece of 4 oz. glass to the shape of the plywood, and then mixed some epoxy. First, I spread in a layer of dookie, then applied the 10 oz. glass, followed by more epoxy, and the 4 oz. glass. I hope I have the shreds incorporated into a sort of fillet.
While I was getting psyched up for this, I stripped the hardware from the boat. I figure I might as well store it that way, saving the trouble for next season's re-varnishing.
I hope this works, and I'm glad that I didn't take the skeg box out.
It seems that the problem was that the box really wanted to cave in & get narrower, despite being glued into place. Next year's box is made out of 1/4" marine okume, and I hope it holds up better.