My buddy and I just got thru doing the same thing this past winter during our down time. Ended up with a Jardine Slip on from KLR650.com, their jet kit and an open elment air filter. Thru many trials and tribulations and some help from those with much more experience and Dyno testing, this is what we are currently running on our Pre 08's, altho the theory will be the same with yours.
Jardine and or Studebaker slip on exhaust from KLR650.com
Used the adjustable Studebaker needle with e-clip on middle position
Kept stock jet, which is a 148 on ours, yours should have a 145. You might have to upgrade to a 148. Stick with a Kawasaki 148 if so.
Eagle Mike said to stick with the factory air cleaner as it flowed best.
Did the airbox mod ie: 5 or 6 one inch holes in the top of the airbox. Make sure not to drill holes past the wall that seperates the airfilter from the Carb intake. Remove the OEM plug from the idle mixture screw and from a soft seat, "means to turn the screw in till it just seats" then turn it out 2.5 turns. The instructions say 3, but that is too much. The Jardine seems a little loud at first, but to be honest, I don't even pay attention to it anymore. They do make an quiet insert for the pipes, an extra $25 or $30. It does make a pretty good difference in sound output, but also kinda kills some of the gained power increase. With these mods, the front end will rise easily with just throttle input in first gear. Some have been able to get 2nd gear wheelie, but I can't with my gut hanging onto the tank, LOL. Hope this helps some.
I know there are a bunch of other exhausts out there that are outstanding, but this is the only one I have experience with.