I'd check the FJR forums. A friend list his 2006 motor at 100k miles and I recall him saying that was normal for '03-'06. That's was about 8 years ago so I don't remember there details. I think '07+ fixed the issue he had.
I know two guys that owned one of these and their experience are polar opposites of each other. One couldn't stand it and sold the bike fairly quickly and the other guy loves his.
The guy that hated it later bought a Africa Twin DCT and loved it. Crashed the first and bought an identical one. He says the Yamaha auto clutch is far behind the DCT auto clutch in refinement. I rode it once and thought it worked OK but I didn't try any slow speed U turns and circles.