I have done this a couple of times and here are my tips:
To open the gear bolt that holds the glass in place simply use a T-20 screwdriver or a wrench with a T-20 bit for more leverage if it's tight and turn
clockwise to open.
Align and tighten the glass in the sealed position with the door closed. There are holes on the door frame that allow access to the screws in the top position. You can see them here
http://s14.postimg.org/js6cza1yp/IMG_0367.jpg and here
http://s14.postimg.org/w0k1a99pt/IMG_0371.jpg.
I did everything what is said on this diy in the same order but I was never able to get the window to go all the way up; the motor seized every time.
This is how I finally got it working:
1. remove the motor
2. align and tighten the glass with the door closed
3. roll the window to the door open position by hand ( if this does not work, then try a different position; all the way down, halfway, sealed, etc.)
4. re-attach the motor
5. wait a while to get out of the protection mode (based on my experience with frozen windows in the winter it takes 10-15 minutes)
6. reset the limits (door closed, 10 secs down, 10 secs up)
7. lock the doors and wait 20 minutes
8. unlock and open the door to see if the window drops
The reason for step 7 is that I was not able to get the window to drop at all when opening the door (it moved up and down just fine using the button) but after leaving the car locked for a while it started working. I think it takes 17 minutes before the car goes to sleep so wait 20 just to make sure.