I don't know this to be so...but in light of four different engines coming from kawi supposedly to account for machining tolerances (the a,b,c,d markings on cylinder and head), there may be as much of a difference from piece to piece in a keihin, too?
Still, with as much performance diff as you could expect from the different engines (none, I would think)..it doesn't seem reasonable that a small difference in a pilot jet would matter. But then, a 1/16 turn of the AS on my bike can make a night and day difference (sorry O&S)...all the way up to how well 3rd gear pulls, and a 10º temp change is certainly noticeable.
Given a handful of the same model/year bike, I'm sure there would be differences between them. Didn't most of the 'problem' go away when you changed reeds back to 'normal'? Are you still of the mind that the keihin is 'wrong'...or just 'different'?
Maybe a good excuse to send the carb off to ron (RB Designs). He does some cleanup in the jet screen/needle jet (different from the jet needle) area. That might: 1. Fix the problem, 2. Make it so much different you wouldn't notice it anymore!! ;)
Good Luck!