Shortly after takeoff and climbout, the autopilot malfunctioned after the aircraft entered an overcast and encountered rain and turbulence. The pilot returned to Bermuda Dunes, CA. After landing, he had the electrical, avionics, and autopilot systems checked. All items were operational. The pilot prepared to takeoff again, but failed to turn on the standby gyro which was battery powered. After departing, he again encountered rain and turbulence in IFR conditions (at about 9500 ft). At about that time, ATC advised his transponder was not providing a return. He switched transponders, but ATC still received no return. Severe turbulence was encountered, the autopilot disengaged, and the copilot's gyros tumbled. He turned on the standby gyro which needed time to be used. A high speed descent was entered inadvertently and the airspeed warning horn activated. The pilot activated the speed brakes and made a sharp pull-up during the recovery. He then returned and landed. Wrinkles were found on the leading edges of the wings.