i've mentioned this plenty of times, but one of the biggest causes of vibrations in my experience is the exhaust. most people just let the pipe hang down and don't strap it to the bike anywhere.
the exhaust can make a sort of "wave" of vibration (for lack of a better term) and as it shakes, it multiplies the vibes back into the engine, and back into the bike.
if you don't believe it, hold the exhaust with your shoe when your bike starts vibrating (a little burnt rubber never hurt anyone) and you can feel it going away.
it's like hitting a big rock with an aluminum bat. even though the rock hits one end, you really feel it in your hands...