How about penetrating epoxy for the lower wood section?
I put some EZ cool over my cab-box gasket, not sure it does a ton. I throw a moving blanket over the hole when we are stopped, kind of isolates the cab.
I want to say I have seen an h shaped extrusion that will go over the ply and leave a lip for the seal to attach to.
As to stairs, is how much space is there for the floor 'frame' Mine had a couple inches there that was enough to mount the hooks for the steps. It would make getting in the box harder though.
Something like this with a landing at the top would make the tool box more useful.
