It does not rise above the height of the metal roof. When it first actuates to open, it actually sinks a touch, then retracts. After it opens a few inches, a wind deflector pops up in the front (on a Gen 2, probably very similar in Gen 1). After it gets to 'almost open' it stops and you have to hit the button again to get it fully open. When closing, it comes close to full close and stops, then you again have to re-key to get it to fully close, where it pops the whole piece up to seal. The seal is really just for wind noise; it's not a weather seal at all and it can/does/will leak, BUT there are four drains that channel the water away from the raised lip of the opening and down through the a-pillar in front (2) and the rear pillar (C? pillar) in back. In back, the exit is inside the trim in back of the rear wheel on each side. Not sure where the exits are for the front two drains, but I'd guess behind the front wheels. I have never had a drop of water come inside the cab.
To clear the drains, the front ones are best done with the roof open (more on this later), from the top, with compressed air to blow down the tubes. They are visible and reasonably accessible from the top. The rear two drains are not reachable, to the best of my recollection, with the roof in any position. You'll have to apply air from below and try to make sure you get flow by checking at the sunroof. As mentioned in previous replies, wire or something else probe-like might work better.
All models can be opened manually. There is a plastic cover that can be removed, believe it, it's there. Be patient and look at the control console for a piece that can be pried off and there will be an Allen wrench receptacle for a METRIC Allen wrench to allow you to attempt to crank the window open manually. If that doesn't work either, the whole headliner has to come down and the assembly worked on from there. It's huge.
Let's say you get it to open and, hopefully, close again. Use silicone spray on the linkage and mechanism. My 95's works just great but gets slower as I neglect it. Once lubed up properly, it works fantastically. Good luck and good shooting.
John B.