I have a 73 MFG Gypsy 15' converted to a center console. I got the boat pretty cheap but its not the "long term" boat that I want. I figured it was good enough to get me out there killing fish until I could afford something bigger. But its good for the meantime. 99% of the floor is solid, but theres a couple 2'' soft patches or strips i guess where the floor meets the hull. At first I thought i would sand it down and run a 4" then 6" strip of fiberglass but then realized if its a little soft it might recrack. Then I thought epoxy resin should do it but its expensive as hell. Now I'm thinking 3M has some great adhesive caulking in tubes that i could butter in there. What would the best way or best 3M product be to band-aid this to get a season or two out of it until I can afford something bigger (more sea worthy) I picked up the boat to putt around the bays, rivers, and local lakes. I could even just throw a 3/4 plywood over it when we use it and remove the plywood when we get home. I also thought maybe drilling some holes and using a can of expanding foam to support it from underneath.
Like what was said above, peanut butter and glass is a correct way to bond the two surfaces (sole/floor and inside coaming). I think I would probably do a little grinding on the two surfaces first so that you are laying glass on glass, rather than glass on gelcoat.. 