What the fermenter needs is passivation.
I fear the pits you see may have come from using chlorine or chlorinated bleach on the stainless. In commercial breweries chlorine is sometimes added to caustic soda for cleaning, but the pH must be > 10 pH to prevent pitting. The rust stains are from where the chromium has been reduced and the surface hasn't reoxidized. Luckily, this is an easy thing to reverse.
What you want to do is circulate a 20% solution of Nitric Acid for 30 to 45 minutes at 120o to 140o F. Then you just let it air dry. The surface will passivate as it dries. After that, you can clean and sanitize it for use. If you can't recirculate it with a pump and sprayball, a simple soak will do.
Do not use more steel wool on the surface of the metal. This strips the patina and promotes rust. If you must use an abrasive, use a non metallic type of scrubby.