I know this means more expense, but if you really want to get it sorted get a Power Commander and a couple of hours with a guy who knows how to work a Dyno. I have done just that with my S4r after doing the airbox and fitting a full Arrow system.
Mine is really smooth, its got better power delivery through the full rev range and delivers more torque, so the mid range, which is after all on the road what really counts is really strong.
