In my newbie opinion, the Dyna muffler is just a cheap replacement for the stock muffler, but some people love them and get them sounding really good... go ahead and hold that candle up to the header gasket seal again to check for a leak, go all the way around the circle, then check every other connection on the muffler, and make sure your idle screw is set right... if your stock muffler is in good condition I'd just change the header pipe gasket seal, or get a Supertrapp, change the header gasket seal, and rejet... and I'm just speculating from my own Dyna experience... I don't know too much about bikes but I know I had my idle screw setting messed up once and I was backfiring so much I thought someone was gonna call the cops...
But remember I'm new to this stuff...