The sunroof on my 2003 F150 4x4 got stuck in the open position today.
Forums say to manually close it you must remove the entire interior headliner or drill a hole at the sunroof motor in the headliner.

I found an easier way.

1. Find two plastic push pins in headliner near interior rear window. Pull out.
2. Rear of headliner can now be pulled down a few inches.
3. Open rear cab center sliding window.
4. Now exit cab, climb into the truck bed, stick hands through rear cab window and pull down headliner. You can now see above headliner where sunroof motor sits.
5. Sunroof motor is right in front of open window in center. There is a white/grey gearbox to the right of motor. On the gearbox is a small hole.
Insert 1/8" Allen wrench into hole, and turn clockwise to manually close sunroof.
6. Re-intall plastic push pins,

It's a little hard to fit hands above headliner and turn Allen wrench, but approx. 15 turns gets the sunroof closed.

This way took only 10 minutes!!! Pretty neat to fix problem while standing in the truck bed.