Sunroof is a bitch.
Remove the Oshit handles, rear view mirror, sun visors, interior light, sunroof controls and carefully remove the rear plastic keepers. Don't use a screw driver, take your time with a real keeper remover (it looks like a pry bar with a v-notch cut out of the middle of the blade). Remove the A and B/C pillar covers and then carefully take out the roof liner. You will see the 4 hoses in the corners. Don't straight blow into them with your mouth, if they're clogged, then you probably will get a little water washing back into your mouth. Use an extension hose instead.
Also, make sure you check the track. If there is anything inside the track, the water can spill over the tray and into the passenger compartment. B13 sunroofs suck, and were designed by a bunch of crack monkeys, this happened to me.
Also, can you see between the rubber seal and the edge of the roof hole? If you can, then maybe you need to get another glass replacement. Changing the rubber seal doesn't always do it well if the glass is rusted badly.