Chances are good that your rear tire is misaligned. If the rear tire isn't tracking exactly straight it can lead to some odd chassis behavior. Double check the alignment marks on your swingarm to make sure they're even on both sides.
In regards to the alignment marks on the swingarm, they're not always correct either. While most are dead accurate, we've seen some that weren't right. In that case, something like a Profi Laser C.A.T. Alignment tool can be helpful in getting everything plum.
Sometimes tire diameters vary between different models and too much front or rear sidewall height can also cause handlebar wobble, so be sure to buy the correct tire size-not simply what's on sale.
More often than not, the wiggles are caused from poor wheel alignment or the wrong profile tire. Also, be sure to check your tire pressures about once a week.