I replaced my mufflers on my ATR SS 2.5" duals a few weeks ago. Cleaned the joints with fine sandpaper...was very impressed with how little effort it took to get them looking perfect after being together for 7 years. I wasn't worried about the look of the finish since I was only cleaning away gunk from the muffler/exhaust pipe joint. Yet it looked great...think I used a 220 grit sandpaper.
Later, used the same paper to clean up the last 10" of the exhaust tips....light pressure followed by some emory cloth and they looked new.
Removing paint will clog the paper pretty quick but a few sheets and you should be OK.
You could test sand the exhaust pipe in a non-visible location.
Good luck, Bob