A noise that goes away when you pull in the clutch is unlikely to be a valve train noise, or an engine noise at all for that matter.
I have read that Hexhead transmissions have a sort of cush-drive on the transmission input shaft (similar to Harley's infamous "compensator sprocket") to smooth out power pulses a bit, and that these have a not terribly uncommon benign failure mode which does nothing beyond make a bit of noise. Can't say I've ever heard that sound myself, so don't know if it's a ticking or not.
There is also a thread somewhere on this forum where a guy spent forever chasing a noise and it turned out to be a loose windshield screw!
These bikes are in many ways mechanically farm implements (though with supercomputer electronics!) and make lots and lots of noises. I have gotten in the habit of simply ignoring "funny noises" if all the routine adjustments are within spec.
Your mileage (and sanity) may vary, of course.
Whizzy brakes, no FD drain plug, what's not to like?