Whent for a ride today and at times a strange noise and vibration through the foot board occured.
I can only explain is as a sound simular to someone throwing a handfull of small nuts at the underside of the engine and a rumbling vib through the boards this also happened once when i depressed the clutch to change gear any ideas.

 

I was helping a friend of mine put on his highway pegs today and noticed the bolts that hold the floorboards to the bike were loose on one side. Not loose enough to rattle, but enough I could move the floorboard. Might not be your problem, but worth checking.