KC--you are saying that I should apply the epoxy before stripping. Will the heat gun harm the epoxy that I have worked down into the crack, or is there a good rule of thumb in terms of distance to keep away from epoxy and outside of that boundary no harm will come? I'll try to work it in, let it set and then when stripping, carefully use only a sander over that area, but heat gun and sander over the rest.
Greenlake--is the system three epoxy thinner than most before setting up? That may be just the consistency I need to get in in the the cracks with a spatula. I've got a really thin metal cake spatula for this that my wife does not know I am thinking about!
As for the thwarts and structure. I do understand--they really should be seated well into place, and that's what concerns me. What is the correct thing to do: try to pull the boat back closer together and then re-install the thwarts? They won't be able to withstand that sort of stress if the hull is really flexing against them, so that would mean cutting the hull or centerboard trunk somewhere, realigning and then re-installing the thwarts. I like your suggestion more, KC, of measuring the difference and making up for it with mahogany blocks epoxied onto the thwart ends, but IS THE BOAT OK BEING SPREAD OUT THAT LITTLE BIT MORE than it was originally? Of course, I suppose it could have been just like it is now when it was new, but I have a hard time believing anyone would have been happy with the fit and finish if that were the case. And besides, that wouldn't explain the bent screws. I have this fantasy of removing the screws and seeing the boat spring back into alignment--that the bent screws were what held it out of whack

Does anyone recommend replacing the thwarts with some other temporary support while I have them out of the boat? They aren't in that bad of shape compared to the combings, but I'd like everything to match.
Thanks!