What a shame. Nice makeover. However..
If I were you, I would NOT spend too much time INSIDE that car with the windows closed no matter how nice it looks on the surface. I would pull the seats out, Pull the carpets, dash and door panels out and start cleaning and disinfecting from the roots up. Mold that bad is alive deep in that car and will reappear at least as airborne spores that can get you REALLY sick. That said...
You can revive it if you do it right. That TR is a diamond in the rough. Certainly its a diamond worth polishing. Please know, experts will always be able tell if when a car has taken on water. Personally that is a project I would LOVE to have. You are lucky to be able to bring an absolute classic back to form. It will be a tremendous amount of fun. Enjoy it. I would.
Joe D