Lots of possible causes for this:
The most common cause of headshake, is the front wheel getting light under acceleration while you're also running over rough pavement. Usually only lasts a couple seconds and then settles itself.
It can also be caused by a wheel being out of balance or something similar. Incorrect air pressure (if it's way too low it decreases trail) in the front tire can contrubute to this, as well. If tire pressure IS low, check for a leaky valve using soapy water or for a nail in the tire, causing a slow leak). A lot of times you can push through a headshake with a short burst of more speed, then backing off the throttle slowly.
Driving hard out of corners can also sometimes cause headshake especially if the pavement is a bit bumpy. The front gets light, the wheel is still turned slightly but straightening out, and the tire interacts with the bumps causing a back and forth oscillation that usually damps out quickly.
Replacing the rear tire with a taller one will reduce trail and make the bike more prone to headshake. Lowering the triple clamp downward on the forks (= moving forks upward in the triple clamp) will do the same thing.
I've read that the R3 was designed for riders in the 130 to 160 pound weight range, so the rear shock should be on the correct setting for you, but you can always try different settings to see if they make an improvement.
Here's a real doozy of a tank slapper
https://www.youtube.com/watch?v=LZ1srcQMa_0&feature=related
