TAKE IT TO THE TRACK !!!
I have a 08 R6, it has a full exhaust, I had a power commander but I need a new one, i've rode it 3 or 4 times without the pc putting on about 120 miles, on the last ride after about 2 min. of riding the exhuast sounded deeper than usual kind of like something may have been blocking the exhuast flow, also it's been hesitating from 4-5k rpm, so if you can be any help that would be great.