The open air filter alone will make it worse plus add an annoying intake "honk" that exits right in your face... but some people seem to like that. :
I think either the Rapid Bike or the Power Commander will do the trick for your S2R since you don't need to deal with the 02 sensor on the 800 motor.
I would call Fred or Doug at
Silverback and see what their current preference is. I think maybe the Rapid Bike has some "auto" features that make the tuning a little quicker, thus less dyno time.