I have a 2004 Night Train with a Wimmer spike air intake and the Supertrapp Phantom 2 into 1 pipe (no baffles of course). I had a Power Commander installed and tuned with my old pipes that were similar. It seems the new pipe backfires more often and way louder. Is there a leak? Am I burning too rich or too lean? Can I use the manual adjustment on my Power Commander to fix this problem?
it is fuel injected.

I am fixing on purchasing my first harley... a Black denim FXDF "Fat Bob". One of the things that they emphasize is the Tommy Gun 2 to 1 to 2 exhaust. I started one this weekend and it sounds like a pussycat. So I have been toying with the idea of sticking some V&H Black Short Shots on...once I get the bike of course. Opinions?
Adjustments...can I just add a power box to it so it will self adjust.
ha ha...I will be running the exhaust with baffles in, I do like loud pipes but it shouldnt be painful to the rider or the guy 3 blocks away.

Bub pipes don't have a pre-drilled hole for baffles. I'm guessing about 1-1 1/2 inch.
While loud pipes save lives and sound good, you need the back pressure for performance. Without baffles, you loose 5-10% HP; carbon up the ends of your pipes & don't burn fuel efficiently causing the 'pop'/flames out of your pipes. Baffles cut down the noise only about 5 decibels & cops leave ya alone if they can verify you have them in your exhaust.

can you remove the baffles from a stock 1200c-2008?