Marine plywood is fine but I would urethane or epoxy coat it to reduce water penetration. I would also not put the fiberglass back in since it holds water. I would use something like rigid foam with a small gap between it and the floor and create a drain path so water won't get trapped between the floor and the insulation. Yes you will need to remove the lower rear skins. It is not that big of a deal. You need to get some clecos to put the panels back on.
This might help you some.
Doing something like this at the back might reduce rear end leak problems.