"My only symptom that I've actually noticed is excessive clatter at 3k (+/- 150 rpm) on light throttle or decel. Not there at 2500, not there at 3500, but very noticeable at 3 grand. Noise sounds very hard/fast/metallic/high up in the engine."
I'm no pro at this, but my semi professional guess (I've been an aviation mech for 10 years and have rebuilt several motorcyle engines) is that 1) it probably only 'ticks' when it's hot (not at 3k when it's cold), 2) oil service is beyond 3,000 miles 3) and/or the oil used is less than 20W-50. More than likely YOUR 'TICK' is during NORMAL operating temperatures. Even a "1 bar" (according to the FJR Temp guage) may be enough to cause the 'ticking' you are referring to. What might be happening is that the oil thins and creates a 'ticking' sound at an RPM that allows the valves to, for a lack of a better term, float. If your valve guides were wearing I would expect to hear the ticking at nearly if not every RPM you ran at. I have ridden many motorcycles that 'tick' at a given RPM (such as my late 79 KZ650, as well as my 05 FJR), but that is no indication that valve guides are wearing. As stated in an earlier post, do you notice oil build-up near the exhaust valves? Take the exhaust off and rub a rag in the exhaust port. If it is extremely wet with oil then maybe it is a valve guilde. Valve guides with excessive tolerances might produce oil in the exhaust ports. For the ticking to be a warranty item I would believe that at least 3 factors need to be present.
1) ticking during most RPM ranges (and getting louder over time)
2) oil build-up in exhaust ports and,
3) noticing oil depletion
Again, it is not that uncommon, during normal temp operations, to here ticking at a given RPM. If it continues into a wider RPM range...say 2,000-5,000RPM; then I might be more concerned. But if it only 'ticks' at 3,000-3,500RPM...That would not concern me.
Just mt $0.02 worth