Here are some common moonroof maladies and fixes or workarounds for them. This page does not cover moonroof rattles.
The only way to manually close the factory moonroof is to completely dismantle the switch console and motor assembly. On '89 to '91 SHOs, you need to push down on the map light and sort of pry the map lights out one at a time. There are two screws under there. Take them out. Then pull the cover rearward and slightly down. The mechanism is then activated by a window crank arm which you will have to buy or locate.
On the '92-'95 SHOs, the relay seems to be the biggest culprit. It's a bit more difficult (and expensive) to replace than a fuse.
Remove the switch console and motor assembly as described above. Disconnect the connectors and you can take it to a table where you can glue the switch back in.
Usually caused by a faulty moonroof relay. The moonroof relay is located under the dashboard. To get to it, open the glovebox and push in on the sides until the glovebox falls, exposing the underside of the dashboard. The relay is on the righthand side. On a '92 it is at a 45-degree angle. It's held in by one bolt and a wiring harness. One caveat: no one but the Ford dealer may sell you the correct part (which, interestingly enough, is stamped "BMW"). It's about $25.
Water inside sunroof
Thanks to Carl Bernhard for the following : > It rained tonight and I had a friend in the back seat. He said he was > getting wet when I accelerated. Upon further examination, water is leaking > in through the passenger side ceiling light. Is it possible that this is > caused by the accident I was in? Could it be from the sunroof? Has anyone > had this problem before?
This is from water accumulating in the collection pan under the sunroof. Normally, it is drained by 4 hoses, one in each corner of the pan so it can drain no matter how the car is tilted. The front ones are visible when you open the sunroof,as holes in the front corners of the sunroof opening, but the rear ones cannot be seen as they are 'way in the back of the pan, under the roof.
The front ones exit behind the front wheels and the rear ones exit behind the rear wheels on most cars. Unfortunately, the ones that normally plug up are the rear ones, just to be contrary.
A collision or bad repair could plug up a hose, but that is not likely. Most of the time the problem is caused by leaves or other debris clogging things up after they decay. Very often,though,the hoses are plugged up by stuff that grows in the tubes all by itself. I guess this is some sort of algae or evil spawn. I have also seen undercoat block the exits.
To find the problem, park the car on a level surface and carefully pour water in the trough around the sunroof opening. Note where it leaks out from under the car. It should produce 4 puddles. By noting where water comes out, and where it does not, you can see which of the tubes are clogged and where they exit. For some reason, many cars have the exits well hidden and hard to access. Of course, this is nothing new to SHO owners.
The front ones can be blown out from the top with an air hose, especially one with a rubber tip or long nozzle. The rear tubes will have to be blown out from below. Be alert up above as a good deal of water and muddy stuff can be blown out. Lacking an air hose, you can try to run a fairly flexible wire up and around like a Roto Rooter (tm). A good tool is an old flexible speedometer cable. Work the wire while you pour water down to flush it out.
Note that the seal around the sunroof panel is not designed to actually stop water; it just slows it down, cuts down on wind noise and fills the crack, so don't spend a lot of money on a new one just because of a leak.
Can you prevent this? Keep the sunroof closed when leaves are about. Flush with water once in a while. Maybe in the humid South where algae readily grows, some sort of bleach mixture might work.