Fuel pressure was checked and is where it should be - the pump and filter are new within last 500 miles. Checked for exhaust leaks but will check again. I did clean the air temp sensor - that one was pretty dirty!
My MAP (Manifold Absolute Pressure) Sensor, the flat one that plugs into the manifold itself, was also really dirty and the gasket showed signs of oil leaking past it. The MAP sensor almost looks like a universal part used across a wide variety of vehicles, including lots of GM products. Strangely the MAP Sensor is not listed on the M3W Alternative Parts List. Anyone know the alternate part number for this one? The S&S Part number is 55-1037.
Just read the ProTune manual on how to reset the adaptive maps so I will do that tomorrow.