copy/paste from the Chiltons on MeL website:
Diagnosis & Testing
1.Ensure that the moonroof panel is adjusted correctly.
2.Check the panel lifter assemblies for obstructions and damage.
3.Measure the voltage between moonroof module assembly C905 pin 1, circuit 400 (LB/BK), harness side and ground. Voltage should be greater than 10 volts. Repair the circuit if necessary.
4.Measure the resistance between moonroof module assembly C905 pin 6, circuit 57 (BK), harness side and ground. Resistance should be less than 5 ohms. Repair the circuit if necessary.
5.Measure the resistance between moonroof module assembly C905 pin 2, circuit 1173 (BN/OG), and C905 pin 5, circuit 1174 (WH/RD), while depressing the open button. Resistance should be less than 5 ohms. Replace the moonroof motor if not.
6.Measure the resistance between moonroof module assembly C905 pin 2, circuit 1173 (BN/OG), harness side and overhead console C915 pin 10, circuit 1173 (BN/OG), harness side. Resistance should be less than 5 ohms. Repair the circuit if necessary.
7.Measure the resistance between the control switch pins as follows:
■Pins 10 & 11 and pins 10 & 12, greater than 10,000 ohms with the switch off.
■Pins 10 & 12, less than 5 ohms with the switch up (closed).
■Pins 10 & 11, less than 5 ohms with the switch down (open).
8.Replace the moonroof motor if switch tests correctly.
and to R&R the motor:
The moonroof needs to be in the closed position. Manually close the moonroof if necessary.
1.Lower the rear of the headliner as follows:
■Remove the overhead console, if equipped.
■Remove the moonroof trim.
■Remove the left and right-hand A-pillar assist handles.
■Remove the left and right-hand windshield garnish moldings.
■Remove the coat hooks.
■Remove the mounting screws and remove the sun visors.
■Remove the B-pillar trim panels, SuperCrew models only.
■Remove the upper C-pillar trim panels.
■Remove the video display, SuperCrew models only, if equipped.
■Disconnect the two rear map light electrical connector, SuperCrew models only.
■Position both front seats fully rearward and reclined.
■Remove the pushpins from the rear of the headliner.
■Remove the dome light.
■Remove the headliner.
2.Remove the three moonroof motor bolts.
3.Disconnect the electrical connector and remove the moonroof motor.
1.Connect the electrical connector of the moonroof motor.
2.Cycle the moonroof motor until it stops in the closed position.
3.Remove the four moonroof panel bolts.
4.Remove the moonroof panel from outside the vehicle by lifting up and out.
5.Insert two 1/8 inch diameter pins through both portions of the moonroof panel lifter assemblies.
Insert two 1/8 inch diameter pins through both portions of the moonroof panel lifter assemblies—2001–03 F-150 and 2004 F-150 Heritage Edition Models
6.Install the moonroof motor and tighten the mounting bolts to 44 inch lbs. (5 Nm).
7.Remove the pins.
8.Install the moonroof panel and tighten the mounting bolts to 44 inch lbs. (5 Nm).
9.The remainder of the installation is the reverse order of removal.
in the R&R section, it refers to manually closing it, but I didnt see where it said how...I would assume something close to the motor, so the best I can offer is to look there