Cecil:
Hit it with a wire wheel in a drill to get the rust removed, then apply the anti-rust stuff that you have. After that cured, I'd put a thin coat of silicone caulk on both sides of the metal, then install the gasketed toilet flanges. Wait 24 hr before adding a lot of water, although you could mist the outside of the seal area with water for a faster cure of the silicone after the gaskets are in place.
That should take care of any future problems.
