You need to get a second opinion the vibes thing. FJRs do have a rough patch around where you describe so it could be normal. Ask one of your FJR owning mates to ride it and see what they think. My 04 has a rough patch in the 3-4K rpm range but it's done it from new and now has 100K km so it's normal for me at least.
Try dis:
RDCU-ATBS
Thanks for the pointer but doing a TBS didn't make any difference IME. The vibration feels like some kind of mechanical resonance. I'm pretty sure Ive seen it referred to by others on here too in the dim and distant past when ticking was all the rage.
Was the TBS a regular one? If so, it was worthless. If the throttle plates were actually adjusted, then that is different.
There are obviously (many) other reasons why you might have vibration. But a ticking valve isn't one of them, so you can rest easy there.