I would go with the power commander especially if you changed the headers, pipes and air filters . That way you are getting the max performance out of you bike. The good thing about the power commander once it is set it is set. Now as the bike get normal ware naturally in a few years maybe 2 or 3 you just attach the power commander to you computer type in your info and load the new setting and it is not hard at all most people do not even do that. On mine every time I check it it is good I had mine on my bike for 7 years never had to tweak it yet. Another good thing is if you get another bike you just get the program for your new bike and program it into that same power commander so it is not a lost at all.

Before I spent money on a power commander I would find out what the problem really is. U didn't say much about the bike ,EFI , carb, go faster stuff, stock ? Its not a temporary fix if u let the Power commander on it. I've had lots of bikes with power commanders on them . To get the most out of them u should put the bike on a dyno. This starts getting expensive.