How many miles on the bike now?
I assume that you know that your trannie will get smoother once it's broke in. I have an 05 and though it's not an AE, many of the basic shifting principles are similar. Mine was a little clunky when I first got it. I just needed some time to get acquainted with it and the FJR needed some time to get broke in. Not sure if this will answer your question, but there's some interesting reading here:
clicky 1.
Needless to say, the tranny is a lot more accommodating if you shift at really low RPMs. However, at higher RPMs the smoothest shifts are achieved when you get off the throttle just enough to unload the tranny, but not so much that you are decelerating. There's a "sweet spot" between accelerating and decelerating where the engine is not pulling the bike forward nor slowing it down. Shifting at this exact throttle setting is REALLY smooth. This is why the guys say they blip the throttle. This takes practice, but it's worth it: it works well. Timing is everything, and when you do it right, the FJR rewards you with a smooth seamless shift. On my bike, if my "blip" it too short or quick, it won't shift at all. As long as the engine is still producing thrust, it will not shift (without the clutch). If I "blip" it too long or too deeply, it CLUNKS. Reason? Engine RPMs were decelerating past the point of no load. As soon as the shift is completed, for an instant, the engine is decelerating the bike. If ya get back on the throttle quickly, the forward thrust takes up the play in the driveline, resulting in the clunk. But getting that blip just right isn't easy. However you will find that if you practice it at lower RPM's it'll come to ya. This principle is the same on an AE or a regular FJR. A little practice turns a clumsy clunker into a master blipper. So, let us know how it works for ya.
Gary
darksider #44