Firefly newwood- View upon completion of plywood rot repair. Replaced rotted plywood with new oak boards of the same dimensions. Used 5200 to bond to the hull. Had to remove the toerail in order to get at the deck-hull joining screws! Replaced and resealed the toerail with new screws (mostly) and 5200, of course.

wow, didn't even realize that this was something that I might have to do. I have taken off the vinyl on the ceiling in the cabin but haven't even begun to locate the chin plates that are located under the windows. this is definitely helpful. Is it as easy as pulling the old hardware, replacing and sealing the new wood, and installing the hardware?

As far as I can tell, yes. I decided not to glass over the inside of the wood. The chopped mat they had in there made a pocket that trapped water and rotted out the original wood. I was able to rip the chopped mat out by hand, so I don't think it was adding much strength.
I relocated a few of the deck screws... originally they were too far outboard, so the screw was actually between the wood and the fiberglass hull, instead of firmly in the wood. I sealed up the old hole and carefully measured the location for the new screw pilot hole so that it would be in the middle of the new wood.
Of course, when re-installing the hardware make sure to seal everything up with your goo of choice. Also, be sure to prepare the wood and fiberglass surfaces that you are bonding properly (follow the manufacturers instructions). My prep involved sanding with a rough grit (~80) and cleaning with acetone.

Oh, I did some interesting calculations when I was deciding about glassing over the inside of the wood:
3M's documents have the shear strength of 5200 bonding fiberglass at 362 psi (the fiberglass bond is weaker than the oak bond, 562 psi). Those wood pieces are 4.5" x 8" each, so we are have a maximum of 4,300 lbs of load per oak piece with a factor of safety of 3. The shrouds are each attached to a different oak piece. The safe load of 3/8" wire rope is 2,440 lbs (according to an internet reference I found). So, there is some comfort for me in those numbers.