I heard the 06 LE's are being recalled so that I can have the only one. You have to take it back and get the Cranberry.
even though i quoted that, this is for the original poster.
i have a "cranberry" ... same issue.. but its a random thud here and there, and an occasional knock, and sputter until about the same rpm you said..
no problem with bladder infections though.
... one thing that helps is to add more oil, and make sure you're running on GOOD gas, preferably at 89 octane.. it seriously helps.. 87 runs like crap, 93 runs like crap, 89 seems to be about perfect, and i really do FEEL the extra horses at 89 (though that SHOULDN'T make sense). The less ethanol the better too. ethanol wasn't as widely used in Japan where these bikes are made, when these bikes were brand new.
Cheveron gas really screws my bike up compared to citgo (but citgo has horrible gas). exxon seems to be pretty much the best in my bike. but... truth is, around here, ALL gas has about 10% ethanol, so that cant be avoided. but something about exxon gas makes my bike run better with less hiccups, knocks, and random crap.
keep in mind though i'm in texas, and gas changes literally from city to city. what works for me may not work for you, gotta experiment.