Why do you want to take the cap off? That is a tricky process as you are finding out. Can you repair the transom w/o removing the cap? Hopefully you can get at all the decking necessary to fix the floor, w/o removing the cap.
The rot under the vents in the transom is nothing to worry about, as I think it will be an inch or so of rotten plywood.. Simply chistle it away and use some marine putty to fill it in. It will be strong enough and not seen with the vent covers installed.
Just my .02
The rot under the vents in the transom is nothing to worry about, as I think it will be an inch or so of rotten plywood.. Simply chistle it away and use some marine putty to fill it in. It will be strong enough and not seen with the vent covers installed.
Just my .02