Abstract: A control system for controlling the stroke length of an axially reciprocating shaft in a double-diaphragm pump between a leftmost shaft position and a rightmost shaft position. In one embodiment, the control system includes a marker on the shaft of the pump. A sensor is positioned adjacent to the shaft and located along the longitudinal axis of the shaft with respect to the marker to sense a change in the position of the marker when the shaft is at the leftmost and rightmost positions. The sensor sends signals to a controller that in turn sends a response signal to a driver. The drive alternates directing pressurized air to a first air cell and a second air cell to selectively reciprocate the shaft in a desired direction between the leftmost and rightmost shaft positions.