My exhaust was in a pretty awful condition. It was essentially rusty and very tarnished. However the big exhaust nuts came off pretty easily with the special tool and everything came apart pretty well. I cleaned it all up using Autosol steel cleaner (a light acid cleaner) and then Autosol metal polish. This is short to write, but long to do.
I used a Dremel tool to clean the nuts- this was probably a little crazy as it was fiddly and time consuming and they are only about $50 to replace but still- the threads were in good condition. It should be noted that I have been buying bulk bags of dremel abrasive wheels on eBay- these are not original Dremel parts, but cost next to nothing. Strongly recommended.