Motorcycle Repair: Burning rich, hooker header, header pipes

Question
QUESTION: Sir,
I have a 2006 FXSTBI EFI i baught it with the hooker header pipes on it and a tune via thr SE race tuner.  Last summer i put a hypercharger on it wihtout changing the tune and really no change in the way the bike ran at all. In november before i put it up for the winter i noticed that my fuel mileage went way down i was getting about 50mpg and it went down to about 35mpg.  Now i got her back out and i cleaned the plugs in hopes that would fix it but no luck and it is running a bit rough just here and there.  Where do i start on figuring out the problem.  I do have the SE tuner programmer for it if that will assist me.  Thanks

ANSWER: When you pulled the plugs what color were they?
Mike

---------- FOLLOW-UP ----------

QUESTION: They were both black and sooty with normal wear they are the original plugs and i didn't check the spark..yet.  When i first start it up cold it will idle hi like it should but it only idles hi for about 2-3 seconds at most then drops down to warm idle speeds and you can really smell the gas then.

Answer
Sounds like your SE tuner is not working correctly and is sending to much fuel. Having the programmer will not help, unless you have a exhaust 02 analizer. You need to have it run on a dyno to see what is happing with the race tuner and see if it can be adjusted.
Good luck and happy riding
Mike