I just noticed your post.
I have never rebuilt a pontoon deck before but from what others have told me, all they do is rip out the old deck and replace with marine grade plywood and glass over it. I understand it is a simple process since everything is either screwed or bolted in. Just remove the rails, seats outside framing, etc and then remove old deck boards. I understand the removal process is the most difficult phase because of rusted screws. Use stainless steel screws only and a small amount of marine caulking with the screws. The aluminum cross members should be in good condition.
Good luck and have fun
Tony B Retired woodworker, among other things.
"Strive for excellence and settle for completion" Tony B