I replaced all of the decking in my boat, carpet and all. I used the waterproof outdoor carpet glue that everyone else did. Also, make sure you check the plywood for any signs of rot. If you need new plywood, I would use treated plywood, and put a few coats of sealer on it to seal it up. I also found, with my boat, that this is the time to go over all the wiring, and make sure it is all in order. If you need to make any fixes, or install any new electronics, its much easier to do when you have the floor off. I also made some modifications on my boat that weren't original, so I was able to tailor it to what I really wanted. Overall, it was a lot of work, but it wasn't rocket science by any means.
