Want to share a story with you on this subject.
I got my R1 brand new in 2006 (2005 model) and after only 3500 miles clear signs of ticking was heard from the engine. I started consulting different Yamaha dealers to get some feedback on why. None of them had the answer - most of them told me it was supposed to sound like that. On the internet I had no luck finding others having same phenomenon. Some weeks ago I met a guy with an RN12-2006 with same mileage and it was absolutely without any ticking at all. So I gave it another shot finding help and luckily found a Yam dealer that had the answer. It appears (without any service-announcement from Yam) that a series of intake-valves lacked proper hardening and hence resulted in much too early ticking due to greater valve clearance (the valve-rod deformed in the end).
He mentioned the possibility of changing shims - but that would only result in silence for a short mileage and then it would start again.
So this dealer actually changed all intake valves under the 5 years warranty (3000$ repair).
Having had a heck of a time finding any help I'm dropping this info here if any of you guys experience the same. In order to have a sound comparison/impression I've posted a Youtube video with before & after example. Its recommended that you listen to it through headphones in order to hear the Hi freq ticks.
YouTube - YZF-R1 before and after valve change
Best regards