Did you see how everything was put together before the gears came out? It sounds like the flat gear with the oblong holes is out of position. it goes under the plastic gear extension socket that fits on the metal crank. Make sure you cycle the motor to the closed position before you re-install it on the crank, which is also in the closed position. Otherwise, the moonroof might have problems like stopping in the middle of opening, not tilting right, and so on.
