Charlie, your best bet would be to call in a professional wood floor restoration company. From the sound of it the floor needs to be screened/sanded and refinished. It is possible to do this yourself, but it can be difficult if you do not know exactly what you are doing and easy to mess the floors up even worse than they are.
I would avoid waxes...these are the leading cause of finish contamination when floors get re-finished.
If the damage is not down into the "wood" but merely with the "finish" a Screen and recoat my be enough.
The floor pictured below (foreground) was a screen and recoat.