My main concern has been heat and a ticking sound, only vibrates above 6000 rpm. I have to take it in and see if Yamaha will fix it under warranty with 13000 miles on a 2002 FJR1300. I had a go around with Yamaha with a transmission defect problem on my FJ1100 back in the 80s.
I agree with this comment, the review is very surprising. I have owned a FJR for 4 years now and just have bought a new one (2006 model).
I have not had any vibrations ever, needless to say that with these powerful engines, synchronisation of the inlet is very important!
I agree with the standard seat, as always motorbike makers seem to forget this important thing (I have bought a Corbin seat).
Never had this power problem in the 4000 rpms. It runs smooth through all rpms!!
Riding the new one, I must say that they have improved on the bike, less heat, and the problems with the shield seem to be improved. My partner is not complaining anymore, she even wasn't aware of the speed (less noise and movement of the helmet).
The brakes are very powerful!! More gadgets that make life easier.
I bought an 06 model and rode it from Seattle to New Mexico with my gal. It performed very well in every way except for vibration. I could not believe the amount of vibration coming through the bars and body and had to fight it for 2400 miles. Made throttle fatigue even worse.
I have read every possible solution on the matter, and have decided to sell the bike and buy an ST. It is really too bad because everything else about the bike I really like. But the motor vibration is easily as bad as my VFR, and much worse than my CBR1100xx. I will try the two remedies recommended, throttle body synch and bar ends. If that doesn't do it, I'm outa here. Anybody want a slightly used FJR?
Bought the 07 FJR in January, and I must comment about the vibration thing. Vibration is non-existent on mine. The bike is incredible.
When experiencing vibrations at the grips, go for heavier bar ends. The additional weight at the tips of each bar will rob the majority of vibration energy. Steel, lead, these all work.
Others have pulled off the alumiminum ends and filled the bars with steel rods, pellets, anything heavy.
It sounds as though your valves need adjustment. I've read that the valve adjustment period for this bike is short, and yours may be due. If your valves are maladjusted then air/fuel can't enter the cylinders as well as it should (resulting in power loss... perhaps at 4000rpm?), and the exhaust can't exit as well (resulting in power loss because some of the cylinder's volume contains CO2 from the last hit of the cylinder, and you then can't burn as much air and fuel in the next hit). The tapping you hear could be the valve stems tapping the cam lobes (or rockers if this is an OHC engine). If the engine is running poorly due to the valves it could also explain the vibrations.
Have your valves checked.