Firecapt,
I had the very same issue on my 2013 Bullet Classic. I got mine this year in Feb. Does it sound a bit like a lifter tick maybe? That's what mine sounded like. After completing the break in (1,000 miles) I noticed the noise had been reduce to just a few seconds of clicking. Now, with just over 3,000 miles, the noise is all but gone. Occasionally, on an especially cool morning, the bike will make one or two clicks until I rev it once, but then it stops and I don't hear it for the rest of the day. Another thing that I believe helped is that I switched to a full synthetic oil at 1,000 miles. This also made a noticeable difference in the smoothness of the gear changes. I attribute this to the aluminum in the engine essentially polishing itself out to a sheen.