Shimmy is not related to frame alignment, but rather to harmonic oscillation. In fact a well aligned frame is more prone to shimmy because it is 'neutral'. A poorly aligned bike will rarely shimmy because the tendency to one side will offset the vibrations that lead to harmonic oscillation.  Shimmy takes place when the riders speed, weight and position on the frame are just right to allow harmonic oscillation.   Typically, a different rider on the same bike will not experience shimmy.  Usually, shimmy takes place at the same speed every time.  Testing has shown that every bike shimmies in a certain set of conditions. It is just a matter of whether the rider discovers it.  Two sure ways to stop shimmy when it takes place. Practice these the next time you experience shimmy:
1) Pinch the top tube with the knees. (Damps out the oscillations.)
2) If seated, stand. If standing, sit. (Changes the anchor about which the system oscillates.) 

The whole system is involved (bike + rider). Since the whole system is involved, changing *anything* might help. We recommend:
1) Move the saddle fore or aft 1/4 of an inch. (One can always change the stem to compensate for the change in position). 
2) Change some other component.  Most will have some component the rider will want to change anyway, perhaps a new stem. Larger tires may also help; change from 700 x 23 to 700 x 25.

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