This whole job can be done in about 4 hours actual WORK time. Check out my process (pics to come soon). This is a '91 Sedan, I know the wagon and even 92up is slightly different.
1) Remove headliner, map lights, "oh s***" handles, rear view mirror (basic mechanical knowledge is required)
2) unbolt all frames around the moonroof assembly (this will not drop the roof, it will just allow access to all bolts).
3) remove all drain hoses, there's one at each corner.
4) remove roof motor ground wire from rear above window. disconnect moonroof harness above drivers head.
5) Begin unbolting nuts around assembly frame. Now the roof will start dropping and you'll need a friend or the top of the seats as support. Don't let the roof drop too far without all nuts un-attached, that's how s*** gets bent.
Now you should have this... (if you have anything else, you're probably not driving a Subaru, go to another forum)
6) slide the assembly over the rear seats towards the back window. Here's where you need to be careful as to not smash the window out or scratch your tint (like me).
7) tilt and slide your seats forward and lower the front of the assy. towards the floor. Pull it out the back door as carefully as you can, unless you like scratched door jambs and ripped weatherstripping. I didn't do it but I can imagine.
8 ) place the assembly on a large flat work surface (duh)
For me it did't matter if the roof was open or closed, you can put a hex driver in the motor and open/close it manually.
9) open position. remove the front screws holding down the rails (everything here is a little cloudy, I did this a month ago, trying my best to remember) There are very few bolts that actually hold down this assy., I think 6 at most.
9) closed position. remove the small brackets holding down each roof cable, then pull the cables out a cM or 2. Then remove the small nuts holding the "stop steps" onto the top of the rails, just in front of the cables.
10) pick and pry (gently) under the rails until the front comes up and the rails are seperated from the pan.
now you should have this...
11) using the items seen above, scrape ALL of the crusty black junk out from underneath the rails and where they meet the pan. This crap'll hit you in the eyes on its way up if you're not careful, wear protection (of the eye variety). Make it as smooth and crap free as you can. Then take 80-240 grit sandpaper if you like, I didn't but it can't hurt , to remove any excess.
Use your shopvac throughout, this junk gets everywhere.
12) Get some good medium reducer or rubbing alcohol or even brake cleaner (anything that will evaporate well) and clean the s*** out of that area you just scraped up. Use a rugged towel, no paper, this should be as clean as you can get it.
Now, this is what I used. I hate doing long jobs and I hate doing them more than once even worse. I wanted to be able to put this car at the bottom of the ocean and have the roof break before it would leak, I think I did that. Use what you like but it needs to be all weather and waterproof (what else does all weather mean?).
13) I laid 3 beads of the stripping and 2 beads of the caulk. Towards the front I followed the contours of the lines on the pan and filled all voids with caulk. Of course I split the center bead where the bolts in the pan are but I kept everything close and snug. After this picture I gently squeezed the whole mess closer together so that the stripping was just adhered to the caulk. The caulk beads are pretty thick too.
I let it dry for 2 days, just to make sure there were no problems. Then I reassembled with the following exceptions.
I left out the "stop steps" as I couldn't get the nuts on as the rails were just too high. No matter, the roof works great without 'em. I just put the nuts on.
I ended up breaking the front nuts so I drilled slightly larger holes in the wind deflector arms (not a lot of room for error, be careful) and put a new bolt on each side. If they are in different spots the deflector will look funny when it's up, so keep them at the same distance on each side.
bolt that thing back together as best you can. If you have to improvise just remember to keep any new hardware away from where the middle of the moonroof passes over, there isn't much clearance except for the far front and back.
If you're in the PNW then you know about our recent storms, plus hey, we live in the NorthWest. Not a droplet, need I say more.
How much fucking caulk does it take to seal this thing!!?? I have had mine out twice now. 1st time it leaked on both sides after. Now it is only (so far) leaking on the passenger side. I ran a HEAVY bead of caulk under the rails & then a bead down each side of each rain & smoothed it in. The ends were also caulked under & around & over. The caulk from the 1st time was so stong I bent the pans in places pulling the rails off to do it the 2nd time. Any ideas? I am getting really sick of this car leaking stuff & eating money & drinking gas. Time to get a putt-putt with no friggin' shit moonroof.
i have this leaking problem too if i take of the factory rubber that is around the glass what can i put around as a replacement mine is leaking arond it. 
