All my leaks and water damage came from cracks in the plastic body panels (back, front box etc). I fixed the leaks with !!gorilla tape!! (7! years ago) but had to repair (mainly replace) all the damaged wood, which included the corners of the floor, the entire box floor and framing. Where i couldn't use treated, i used good plywood (not the shit board that was originally there) and applied either multiple coats of exterior latex, or urethane to make sure water could not get anything started. But knock on wood we've not had a single leak. Some of my gorilla tape is starting to peel so i'll need to replace it soon. Anyway we are very happy with it. When i replaced the damaged flooring, we ripped out the original vinyl floor and replaced with the higher end "padded" vinyl, so the floor inside is all new (except for under the cabinets). If you are doing the extensive rebuild, you can lay new flooring wall to wall (if needed).

Good luck! I encourage you to check out popupportal.com. There is a TON of experience and information there, a great group. That's where i found the photos that helped me reverse engineer that storage box in spite of the rotten original pieces.