The sunroof has four drains, four hoses that run from each corner of the drain basin below the roof, down each pillar there, to the bottom of the body. I have hunted leaks around the sunroof's many times, and the 2nd gen and 3rd gen use the same sunroof glass.
You should be able to figure out if the drains work okay. Open the sunroof fully(and remove the key), then use a water hose running very slowly, put the water in the drain basin you see there all around the roof opening. You should see the four holes. The hoses attach above the headliner, so if they are detached, the headliner would have to come down.
If you find out that the drains are clear and flow fine to the ground, then the sunroof glass is the likely issue. There are a few seams in the drain basin, it's not one piece, but those are very unlikely to leak. I thought my issues were from those seams, but re-cleaning and sealing them did no good.
The sunroof glass has an outer seal on it, a molded part which is huge and not removable. The underside is molded onto the glass, so there's no replacement part etc. The seal there on top where it overlaps the glass, that is where it lets go over time. Some may never leak, but I'd guess that most will given 20+ years.
I came to this discovery a couple of years ago. I worked hard on fixing my black 98's leak(headliner in two places). After a lot of time, I RTV'd the entire glass seam to the roof. That didn't fix the leak. I already had the windshield front edge taped over with clear packing tape. The leak persisted, so all that was left was the glass seal/seam itself. I RTV'd that, and the leak stopped.
Long story short, spend some time carefully taping off that glass seal seam. Leave about 1/4" or so exposed of the glass and the rubber seal. Then apply a thin layer of Ultra Black RTV between the tape. Spread it with one finger if you like, it just needs to be thick enough to hold well(1/16" is more than enough), and smooth enough for your liking. It can be done in less than five minutes, and the typical $8 tube will be enough. That results in a seal stronger than the original, and Ultra Black can withstand full sunlight for decades. Don't scrub it when washing like you want to rub it off, but it will take normal washing or a car wash just fine. It won't be pretty, but how many people climb up onto your SUV to look closely at the roof?
