when I had mine I just took the threaded rod off, and never put it back, I used a flat Alum plate under the cleat instead.
As for the rot you are going to have to lay on your back!! Mine was wet but not rotted. Best way I guess is to cut it out from the inside till you get good wood,( leave the out side not cut) square it off to cut a nice new piece to put in there.
Let say you make it 12 x 12, now coat the new piece with resin and while wet stick in the new hole you made, using a 2x4 or something to wedge in there till its set. You could put a few temp screws in thur the top and just fix the small holes after.
Then just add cloth till you make it the same thickness as the rest of the liner. Good news is no one is ever going to see it so you don;t have to be a pro at it. After you are done the carpet will not get wet any longer stopping the mold.
Fill the screw holes on top, if you went that root with some marine tex, and call it done. Now you can add your new cleat, use plenty of 5200 on the screws, (put Blue painters tape down first, then 5200, this way you peel the tape off while still wet and have a clean install) and around the cleat to water proof it! Don't forget the new backing plate for the cleat, can be what ever, but alum in the best choice IMO, just use some anti seize on the screws to stop the different metals from corroding over time.
Some of the glass guys will be here soon to help you, this is just my non pro fix, but it will work! Good Luck