First off, thanks for sending those pictures of the interior and engine. And for being very up front about the floor and transom issues.
Since you are the original owner, they say there is a lifetime limited warranty to the original purchaser (only.. it's not transerable). http://www.lundboats.com/wp-content/uploads/catalogs/2005.pdf
look at page 2.
I love the marketing terms they used instead of saying that the deck and floor are wood. They say "environmentaly friendly material".
And for the transom material they say "heavy duty transom".
I have dealt with rot in a boat before. The fungus that causes wood rot gets into everything made of wood, and it loves moisture and heat (ie our N. TX weather). I found a soft spot in the floor of our 1990 Searay 220 OV. that was just the tip of the iceberg when I started tearing it apart. Stringers were gone, as well as most of the floor (the foam they used for floatation was "Open celled" which is the kind that absorbs water). I got lucky in that on my boat they left a 1/8" gap between the end of the stringers and the transom. The rot needed contact in order to move to the wood in the transom. The boat was only 7 years old and I was the second owner, so no warranty. I never had it stored outside, so the water got in while the first owner had it.
The cost to have it repaired was astronomical, so I took on the project myself. Two years of weekends later, it was back on the water better than when it left the factory. I learned I really hate wood used in boats. They "encapsulate it" in fiberglass, but then put screws into the deck and don't seal the screws. The water wicks down the screws into the wood, and that starts the rot. Same for not sealing the transom with 3M 5200 for everything screwed into it. Using silicone on the big bolts holding the outboard on is just a big leak waiting to happen. Same for transducers, ladders, drain plugs, etc.
So in 2008 when we bought our next boat I made sure it had Zero wood in the hull, deck, and any stressed member. Found a 2005 Voyager 25ft triple Pontoon with 2006 Honda 225hp on it that fit the bill even the deck is aluminum, all seats are roto molded plastic. There is only two pieces of structural wood in the boat. They are both in the console to support the steering wheel.
So when I saw you boat, I thought I had found another aluminum boat with no wood. Was very surprised to hear it had wood in it when you told me of the issues. So off to the internet and I found that catalog.
Let me know what you find out from the dealer tomorrow. I will buy it if they will fix the transom and floor.