You are right that the jetting for the 906 can be improved. I run a straight thru' exhaust and a competition air filter with my Paso so any changes to my Weber jetting may not be suitable for yours. Send me a message with an off .org email address and I might share these settings with you (developed by racing).

I never found the throttle response that poor when I first rode my Paso, but I did step off a Honda NS400R. The standard exhausts won't help but check the idle screw jets (amount of turns out). Check also that the throttle injector pumps aren't blocked - this can happen when the 'bike is stored. My Paso doesn't really move below 3000 so don't think that yours is off tune if you are expecting it to take off at 2000. The changes to my Paso jetting are geared towards high rpm power delivery anyway and there a number of other mods to be made to improve the firing. Try Bauke Meidema's electric relay mod to the ignition unit for one, and I recommend changing the standard ignition coils for Kawasaki GPZ500 units (greater primary coil impedance - preventing overloading of the ignition unit).