Originally Posted by T^2

The first mistake here is thinking that "Auto Tune" is actually "tuning" your bike. It doesn't. Thinking that "Auto Tune" will make all the necessary changes for new cams and intakes "automatically"? Not likely. The PV is a tool. Understanding what the tool can, and cannot, do is important to using it effectively. "Auto Tune" is primarily an attempt to calibrate the VE tables. That's it. Well at least on Sporty's. On BT's - if I remember correctly - it''ll take advantage of the knock sensors and make some (minor) timing adjustments.

Sounds to me like you need a map that's been created for the changes you made (or that is pretty close). I might call Jamie at Fuel Moto. He might have what you need and might be able to guide you through.

Otherwise you might want to find a competent/professional tuner.