You don't have to remove the movable windows to get the vent windows out. Once you've got the bottom bolt and the two top screws out, remove the beltline molding on the door (the one that wipes the window as it goes down), put the window all the way down, and then grasp the vent window and pull it back until the rubber gasket is free of the door frame, then up and out. It brings the forward window track up with it. At the very end, the tab on the track where the bolt went will need to be worked around the corner of the window glass, which is why you had to take the beltline molding off.
Installation is the reverse...etc. Make sure when you put the new one in that the rubber gasket is seated correctly in the door, and that the window is really all the way in.