I hear you on the "do-it-yourself" angle - some of the more unscrupulous shops would probably just slather that muffler sealer over everything and call it a day.
One thing worth mentioning, although your setup is different from mine - I replaced the factory donut gasket with a flat gasket per the instructions for my Perrin 3.0" catback, since it was mating with a JDL front-pipe:
Since you're still using the stock midpipe, you're probably supposed to be re-using the donut gasket, or maybe it'd be worth picking up a replacement donut and giving that a try? Does it look damaged?