If I remember correctly, to remove the quarter pop-out windows you will first remove the plastic sail panels to gain access to a large screw towards the latch end that's holding the window frame in place. There are also a few small screws hidden underneath the rubber seal that separates the quarter windows from the door windows (top and bottom).
Once you get the quarter windows removed, you'll find a handful of screws along the length of the roof rail (again, underneath the rubber seal). There will be a seal sandwiched between the roof rail and the roof, and you will want to replace it. When you put everything back together, to check at the very far rear end of the quarter window and make sure the weatherstrip makes GOOD contact with the roof/body channel. I had to double up the thickness of weatherstrip to seal it properly.
Jerry