miss firing and backfiring

Im new to the buell world, I did alot of reading on them before purchusing my first Buell. I fell in love with it as soon as I road it. I didn't have any problems when I went for a test ride, everything seemed perfect. Later that day I drove city and country roads. Then took it on the freeway and when I got off the freeway it started to spit and sputter. When I got home started reading some forums and everyone was talking about ecmspy. I got lucky and got the cord and disk when purchased the bike from previous owner. Alot of people were mentioning a tps reset. I reset the the tps and it got better but still spits and sputters every once in a while when I roll on the throttle at cruising speed. I also checked the plugs and they are a little black but didnt seem to bad to cause the problem. Going to HD in the morning to get new ones anyways (who knows when they were changed last). I wasnt to sure how to really mess around with the ecmspy, couldnt really figure out to diagnose any codes (wouldn't run any test when I pushed start). Need some advice to solve this problem and any other ideas to check. here are my mods

force winder intake
force one exhaust
dynojet power commander
race ecm

Congrats, welcome. Where are you located?

welcome to the forum.
get rid of the power commander and see how it runs.

mine was doing the same thing now it wont run more than 10 min and starts cutting out and fouling plugs. realy black. maybe the mass air flow sencer? mad power comander? o2 senser? dont know yet any ideas 2001 thunderbolt s3.

get rid of the power commander and see how it runs.

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welcome to buellxb

2nd person to tell me to try it without the power commander. i will next week . it sucks to have to figure out when you can get a couple of hours free isnt