Any suggestions or ideas to protect whats left of the exposed plywood?
Yeah. You don't even try.
At 31... if the underlying chassis is mechanically solid and reliable enough to justify a real renovation then then you do just that.
Take it all down to the steel and install an entirely new plywood flood (with thin sheet metal at the wheel wells) and go from there with all the interior fittings and appliances similarly evaluated with a cold jaundiced eye whether you save and restore or simp[ly start over.
Having that open access will make all the other still inevitable chassis work that much easier to do too.
Just like a house it all starts with the foundation.
If it's not mechanically solid and reliable...
duct tape, quick stuff foam, gorilla glue, baling wire, marvel mystery oil, far too many tools and a few other such things will be taking up valuable storage space.
"the better part of valor... is discretion" (paraphrased from WS)
Good luck whichever way you go.