A rotary actuator position sensor comprises a target with a target surface coupled to a rotatable shaft and a sensor positioned to face the target surface. The target surface is configured to vary the distance between the target surface and the position sensor as the shaft is shifted from one rotational position to another. The sensor provides an analog output signal that corresponds to distance to the target and therefore to the rotational position of the shaft. A controller processes a signal corresponding to the sensor output signal to determine the rotational position. The controller can control the rotation of the shaft from one rotational position to another. The position sensor can be used in a wafer processing system with the controller also controlling movement of a wafer cassette holder into and out of wet tanks and between tanks. The controller can also control an optional agitator and front to back and back to front movement of the shaft.