On the seat issue, I used 1/2 inch marine plywood on my deck and put a second layer of 1/2 inch marine plywood as reinforcing underneath the deck (also attached the reinforcing to the stringers) where I would put a pedestal. I haven't decided on the redesign of my seats but I may box underneath the Captain's chair for added storage. The extra layer under the deck gives a lot more rigidity in the floor and flexibility in how I design the final mounting. My deck has foam under it as well.
On the wet foam issue, my foam was wet so I removed it due to stringer replacement starting in the back to work my way forward (replacing transom, then engine bay stringers, then forward stringers to just past amidships before finally getting to the front section in the V Berth). It took me better part of 2 years part time. All during that time and 2 years before, the boat was in dry heated storage and the front floor section in the V Berth had a hole open to the air. When I finally pulled up that front section, the foam was saturated and still had standing water under it. It hadn't dried at all during that whole time. Just my 2 cents but I would replace it all.