Re-Jet??
Did you?? You need to jet down after making these changes.
After adding a FMF Turbine Core II, Torque Pipe, and drilling my airbox lid, I ended up jetting down one on my main and pilot, and dropping my needle down on notch.
It went from a bike that couldn't pull top gear, to a bike that was happy where ever I was running it as far as RPM's.
I live in Northern IL, at about 1100' or so above sea level.
Check your plug.. If it's black and oily, you need to rejet.