I run TuneBoy in my bike but I think I read, recently, where the standard tune be in place before installing a PC3?
Whilst on the subject of overheating, I installed the 3 K & N's over the winter and yesterday noted that one of the mufflers (TOR's) is so hot that the exhaust gasses literally burned my hand from holding it close to the end of the pipe. The other two mufflers were running cool. Weird since the system runs 3-1-3 so all exhaust comes from the same place, not individual cylinders. It is the top righ one BTW.