There's really three (over simplified) types of tapping noise an engine can make. The higher pitched, more of a clicking, is the injectors and is normal noise. The next is a lower pitch, more of a clacking, is the valves. A slight clack is ok, a loud clacking can indicate the need of a valve adjustment. Then there is the dreaded knock noise .... low pitch knock is always bad and can be rod bearings, wrist pins or worse. If you hear it while sitting on the bike it's probably just the injectors firing, and if you had the valves adjusted after 10,000 miles there shouldn't be anything to worry about. R3's are very noisy engines, that's why they make loud exhaust. LOL
I use a mechanics stethoscope (like a doctors except it has a rod on the end) to tell where noises are coming from, you can also use a large screw driver against the ear to hear internal noise. It's always a bad idea to listen to a diagnosis over the phone or internet, so I'd either poke around with the stethoscope idea or have someone mechanical listen to it.
Auto parts stores usually sell a mechanics stethoscope, not a bad tool to have around.