The floor is a major component of keeping the chassis "square." Thus, you must thoroughly block the coach to prevent any type of movement before replacing the plywood. (Note: That access hole in the floor behind the rear wheel is to get to the OEM HVAC compressor. Don't seal it with the new floor - send me a PM for the reason why.)
You'll need LOTS of bolts & nuts!
IIRC, the seat tracks are tack-welded to the bulkheads.
Since you've got the coach stripped to a shell, after you replace the floor, seriously consider spray foam insulation. Best bang for the buck. If you've got an 18-wheeler trailer repair facility nearby, talk to them about the guy who spray foams the reefer trailers after they're fixed.
Please don't put a fiberglass cap on the rear - it ruins the "classic" lines of the 4106. Just paint those glass replacement panels gloss black so they look like smoked glass. Ditto the front destination sign - matter of fact, if the mechanism is still there, you can get a new roll sign curtain for it and choose your own "destinations!"
FWIW & HTH. . .