A method of controlling a horizontal directional drill having a rotary drive system. The rotary drive system includes a variable displacement pump providing pressurized fluid to a motor, a displacement control that adjusts motor displacement, a torque limiter valve that opens at a torque limit to provide pressurized fluid to the displacement control to allow the system to limit torque, and cross-port relief valves that open at a cross-port relief pressure to limit pressure applied across a motor inlet and a motor outlet. The method includes adjusting the torque limiter pressure to vary the maximum torque applied to a drill string based on operating parameters of the horizontal direction drill, and adjusting the cross-port relief pressure to be higher than the torque limiter pressure each time that the torque limiter pressure is adjusted.