A valve control system includes an engine speed control module that determines an engine speed and a desired engine stop position. A piston position module determines a desired stopping position of a first piston based on the desired engine stop position. A valve control module receives the desired stopping position, commands a set of valves to close at the desired stopping position if the engine speed is less than a predetermined shutdown threshold, and commands the set of valves to reduce the engine speed if the engine speed is greater than the predetermined shutdown threshold.