A method of producing a compensation signal to compensate for misalignment of a drive unit clamp element can include applying a clamp element drive signal to a drive unit clamp element to engage a mover element. A first displacement of the mover element can be determined. A first compensation signal to be applied to one or more drive unit shear elements can be determined based at least in part on the first displacement. The first compensation signal can be applied to the one or more drive unit shear elements and the clamp element drive signal can be applied to the drive unit clamp element. A second displacement can be determined in response to the application of the first compensation signal and the clamp element drive signal. The second displacement can then be compared to a preselected threshold. For a second displacement less than the preselected threshold, combining the first compensation signal with an initial shear element drive signal to produce a modified shear element drive signal, and for a second displacement greater than the preselected threshold, determining a second compensation signal to be applied to the one or more drive unit shear elements.