I have two 98's that leaked past that bonded glass seal. It took me a long time to identify it, and my latest 98 doesn't leak through that yet that I know of. The water gets passed the glass seal and comes out underneath, above the headliner(not above the drain pan). That leaks onto the headliner.
I bought one spare sunroof glass from eBay two years ago, from a 2005. I'm not sure if all of the 3rd gen's(2002-2005) are identical, but that was the impression I got when I hunted it then. I think they are.
But the real issue is that seal being made onto the glass, I don't think it is available apart. I have not looked at the bottom side to see about sealing it with RTV, but I did seal both of my leaking seals on the trucks, with Ultra Black. The first I was not careful and was mad at the leak, not positive it was the glass/seal bond, and I sealed over the gap also. I had been using tape over the gap, and that obviously didn't stop the leak going under the seal.
So the 2nd truck I taped off the glass just inside the seal perimeter, and RTV'd that glass area and onto the seal. It isn't pretty, but nobody will see it, and it will last for ages. If that could be done underneath instead, that would be neater to do, but I doubt it can be done that way.
