Once it was all cleaned the next step was to apply a rust converter. I used a product called RustMort. What this does is it takes any existing rust and chemically neutralizes it.
What you do is pour some RustMort (there are several other brands that work just as well) on a small rag. Then wipe down the entire exhaust with it leaving a good coat of the stuff behind. I then let it dry for 24 hours. Thebadly result was all the rusted areas turned white (some rust converters turn black). A little side note WEAR GLOVES. The chemicals in the RustMort are STRONG and will irritate skin badly.
A picture of a section of neutralized rust on the piping:
Once the rust converter dried I wiped everything down.