Side windows? Its a while since I looked at mine ..Could easily be some more screws under that fat rubber beading you may have not pulled out yet?The actual frame onto the body under that is almost sure to be rusted...its a common problem because the frames are really lightweight non galvanised steel and they rust like crazy...I think the glass where it is "hinged" on the centre pillar just sits there tight...and once you have disconected the catch...just screws..and removed the internal trim the glass "should" come out..
If you have external rust you will need to take the external chrome trim off to get at it properly..a bastard if the trim is bent or the clips are crappy ..Interior wise the water usually runs down the inside of the car just under the removable plastic trim panel to the side of the seat and pools in the floor section under the back seat..smells great!..not..Good luck..