The moonroof problem you and others have described sounds similar to the prob I'm now having with my '98 SVT.
Two weeks ago, I noticed that, when closed, the rear of the MR came to rest about 1/4" below the roofline.
Three days ago, when retracting the roof to its full-open position, it began to stop mid-way, as though it had traveled to the end of its path. The same thing happens when closing it. Also, when tryng to pop it up from closed to vent position, it goes nowhere. Instead, I get a ratcheting sound, and have to nudge it, to get it to raise into position. From what I've read on this BB, it sounds like the gear is on its way out.
The motor was replaced under warranty about a year ago. The car is now out of warranty. Other than making myself a major pain in their butt, do you (or anyone else who reads this) know if I have any "offical" leverage that would compel Ford to replace the motor again?