Don't stop because of one FJR experience.... for all we know, that FJR had badly out-of-synch throttle bodies, which is a main source of vibes on the FJR.
I have assembled dozens of FJRs over the years, and some desperately needed a good TBS right out of the crate; or certainly at the initial 600-mile maintenance.... and if it's not done, can lend a significant amount of vibration to the handgrips and footpegs.
Too, there are a plethora of handlebar risers out there for the FJR (including 2006 models) that might help mitigate this issue for you, if handlebar/grip orientation is a contributing factor.
The bike is too good to stop interest after one ride on a bike that may or may not have been in an optimal state of tune.