SGG - first, welcome to the forums - what part of the country are you from?
As Fx says, whenever you make a significiant intake or exhause change (you mention it too) you should consider having your map updated. By checking the color of your plugs (White is really bad - tan is often prefered) you can tell how the change has affected your engine performance.
I don't know if they are available for your bike, but some people put "torque cones" in their harleys when the go to straight pipes - staff should be able to tell you if they are available for your scout.
If staff doesn't respond sometime today, send your question to J&Ps technical staff through the "customer service" button above.
Hope this helps
The first tool out of the box should be the "book"