My two bits worth. I don't think you're still running the stock pipe, are you? But, just in case you are, the little screws that hold the heat shield on will make a little vibratory, buzzy noise occasionally. It was mentioned before, but is easy to miss.
I guess the only rattly experiences I had on mine were the heat shield screws, from the first time I rode it out of the shop going home. I heard it the moment I started the bike. I rode it home anyway, can't sweat the small stuff. I didn't find out what it as until I pulled the pipe to replace the muffler. I had a couple of hundred miles on it by then.
The other vibration s when the tank bolt loosened up. That was rather intermittent for awhile, too, but it got worse and lost the intermittence when I was out in the desert about 150 miles from home. Not a fun ride home, but detecting the source was pretty easy when I got there. The nut had dropped down into the little square boxes on top of the gearbox.