So finally got everything back together. Here is a review for anyone that finds this thread in the future.
1. The hole and **** style is only used in post March 2006 and 2007 models. Jeep has a service bulletin on this design where if they break, Jeep would replace the regulator and window with the older 2002-2006 style.
2. As to getting the unit out. My solution was to safely use a large flat head to the underside of the plastic **** and force it up and back.
3. As to getting the glass reattached it will work better if you do not fully attach the control arm, leave it loose so you can manipulate it up and down in the slots then drop the window to nearly all the way down. You can then get the hold to line up and eventually pop the plastic **** into the hold.
4. Put everything back together as before, lecture everyone to not slam the doors and don't overly use the rear windows.