Does it seem to change the way the bike rides? Like, any flat spots as you run through the rev range? Feel extra vibes through the bars?
My bike always makes noise, but I've gotten used to it. Keep in mind, even with 12k miles the motor is still changing. "Break in" might be over, but that's still a pretty fresh motor. If you are worried about it, take it to a shop and get them to just take a listen. I wager you could find a mechanic that won't charge. They usually have those stethascope things with the metal stick that lets you listen really close to any part of the motor without taking anything apart.
Or you can grab a broom stick, put it against the heads and put your ear on the other end. Problem is, if you haven't done this before you won't really know what to listen for, but it works pretty well and might give you more information.