Well the well certainly needs to be capped correctly. The area needs to be ventilated to the outside. I would install a moisture barrier and stone. The three season porches i've done I insulate the bays, and also install 1/2' ply from below to keep critters out. In my own home I used 1" foam board underneath the whole thing, then the 1/2". Install subfloor, then flooring. I would make clear in writing that the possibility of the floor moving is high.
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