Just some quick background. Bought the bike about a month ago it has 5500 miles and is stripped of all street legal stuff. I have ran the bike for two track days and love it. Have not had any issues other than I accidentally hit the switch that turns on the auto tune and it killed the battery. Replaced it with a new one and went on with my track day. I started the bike a few days ago and it was running a little rough. Feels like it might be down a cylinder or just weak. Once I get to about 5k whatever it is starts working and it runs out like normal. It is a bit of a hit and miss deal. Sometimes it will run fine then out of the blue it starts running a little off. I have tried running it with auto tune and it still acts up. Not sure but it seems to do it after it gets warm. I am replacing the plugs tomorrow just to start with the easy stuff. Any ideas what it might be?

add on parts
full yohi exhaust
power commander v
power commander auto tune