A control system includes a pressure control solenoid and a flow control solenoid having an input in fluid communication with the pressure control solenoid. A piston adjusts a position of a shift fork and includes a first area in fluid communication with the pressure control solenoid and a second area in fluid communication with the flow control solenoid. A fork sensor senses a position of a shift fork. A slip sensing module estimates slip acceleration between an input shaft and a gear. A flow determining module generates a flow command for the flow control solenoid. A sync control module determines a slip acceleration profile including an estimated slip acceleration, adjusts the estimated slip acceleration based on the measured slip acceleration, and generates a pressure command for the pressure control solenoid based on the adjusted slip acceleration.