A method for controlling a manual transmission includes using a controller to determine a desired torque transmitted through an input clutch and a desired clutch slip for the desired gear after a shift lever is moved to a desired gear position and while a clutch pedal is being released for engaging the clutch; measuring torque in the vehicle drive assembly; using measured torque to determine actual clutch torque transmitted through the clutch; and reducing torque error using the controller to adjust a clutch actuator such that a difference between the desired torque and the actual torque is reduced. Slip error may also be reduced by adjusting the clutch actuator to reduce the difference between the desired slip and measured slip.