(putting in hardwood floors, tile, drywall, etc...)

Lets says worst case it needs a new piece of plywood, 40 bux, and one sq of tile ( its 10 x 10 so should be more then enough ) thats 120 bux, If this makes your deal no longer a deal, well then it wasn't one to begin with.

Favorite durability improvement- tile or vinyl flooring.

Examples of what it needs: new windows, hardwood floor refinishing, doors, tile kitchen floor, light and bathroom fixtures...Any thoughts appreciated. 

Tile has finally gone up in the bathrooms. 

If flip, then granite counters and glass tile backsplash.

Tiled out walk in showers, huge custom walk in closet, kitchen backsplashes, and a lot more. 

I really will have to come up with a creative solution if I cant remove the stain as the rest of the house is a few days from completion and the shower surround tile/glass door etc are already in place.

I would coat the walls, floors and then maybe carpet or tile on top.

If you were doing hardwood I would do it throughout, because that will bring much value.I did a lot of research on luxury vinyl tile and it really doesn't increase property value.