Re: rotted deck and stringers
You really need to sit down and spend a lot of time reading through the restoration forum. I've done two boats now, and I'd be willing to bet you've got a bad transom as well as what you've found so far.
For the materials to use, it just depends on your boat. On one of mine the original stringers were 2x4's and 2x6's so that's what I used for the repair (with fiberglass over it of course). On my Checkmate the stringers aren't really structural, more there as a deck support, so I used 1X lumber with fiberglass. On many other boats the stringers might play more of a structural role for the hull and require marine plywood as the core material. Transoms are ALWAYS marine grade plywood because of strength considerations.
The foam is 2 part pour foam, 2 pound density. US Composites sells it, along with all the fiberglass supplies you'll need. For the fiberglass resin, epoxy is far superior to polyester in terms of water resistance, adhesion to existing fiberglass, strength, and ease of use/mistake tolerance for those with less experience. It costs more, but IMO is worth it.
But again, spend as much time as it takes looking through other rebuilding projects until you know where you need to go.