below 3000 rpm

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Other than behavior, is there a reason to suspect timing is off? Recent valve adjustment service, CCT change? Clattering noises on tight side when engine is cold (bad CCT)? If not. I would look at some of the other possibilities first, including stuff in this thread and what I posted in your intro thread.
My thoughts exactly - in John's case, the previous owner had just done a valve adjust and messed it up. If your bike hasn't had the cams out, I would start elsewhere. With John's bike, my first suspicion was the battery since my FJR runs like crap when the battery is weak. The big difference, though was that his bike was running very rich.

Checking the cam timing isn't that hard but it's not easy to see the cam marks with the engine in the bike. It takes a mirror to really see it.

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Fixing the problem (if it is out) is much harder. The FSM is pretty good for these bikes and a great investment if you don't already have one.
 
Checking the cam timing isn't that hard but it's not easy to see the cam marks with the engine in the bike. It takes a mirror to really see it.
Yeah, it would have been nice if they had put the marks on the inside rather than the outside!. Suppose this way is easier in the factory when the engine is out of the frame. Next time I have to take a cam off, I'm going to scribe a corresponding set of marks on the inside!
I would add that the cam mark alignment with the engine case is with the engine precisely at at TDC as verified by the marks on the pickup rotor.

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Exactly, I think that is where the PO of John's bike got it wrong - with the cams lined up, the crank was off one tooth. Easy mistake to make but turning the engine over a couple of times and double checking should have caught it.
 

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