I know there's soot, but that doesn't mean the mufflers get extremely hot, especially for everyday driving. Since they don't burn up, multiple coats of any high-temp clear coat on the muffler should help preserve the look after you bring it back to the state you want it to be. I know this works on headlights, as well as some other surfaces. Give it a shot! I know gravel or rocks getting kicked up may go through the coat, but you can definitely try, and if all else fails, find a high-temp epoxy to coat it either on top or instead of the clearcoat.. Look into it! What are the chances that multiple pebbles are going to get kicked up to the exact spots where you build up the clearcoat to protect it - especially those spots which are more prone to surface rust as the ones you see now. Those are the areas that will need extra attention. Look everywhere, including searching for different clear sealing compounds online. Here's two words to help you start - "Polyurethane" and "McMaster-Carr" Please rep if you find this to help you eventually.
I guess this doesn't exactly help refurbish your muffler.. But hopefully it will help keep it that way after you are about to put tons of elbow grease into making it look nice!
Another thought - if you do end up sealing it, use sealer on muffler only - leave tips the chrome and untouched, because they will never dull or rust as long as you clean the soot off periodically, but if you use clearcoat, there is a chance of it eventually flaking, and again, looking at the tips close you would be able to tell that they have been covered with something, but no one will look that close at your muffler itself.
