It's been a while since I did mine, but I had to replace the glass in my 2nd Gen's tailgate, and I remember being able to bypass the window lock-out. I believe the locking rod disconnects near the mechanism's pivot/hub, allowing the lock to release regardless of the window's position. Regardless, you will still need to lower the glass at least a little, so it can clear the guide channels on the window frame. As for the window controls, that is very typical of this model--the window supports tend to rust out, to where the motor can barely move the mechanism. Once you get it apart, you should replace the whole mechanism (so you can lower the window properly--otherwise you have to leave the tailgate unlocked all the time).
