I assume you have taken all the "visible" bolts loose.. There is a catch on the bottom of the window you have to take off to allow you to get the window to come out the top. There may even be two,,, It's been a while. look along the bottom of the window frame.
There is also a stop on the back of the window. you will need to take the allen screw loose.
There's a front uplock and a rear uplock. The front is attached to the lower window frame with a 5/16" hex bolt. Remove it. The rear is attached with an allen screw accessible from the rear edge of the door. Rubber gasket comes off first. Undo the allen and reach up and grab the rear uplock assembly. Remove it. Remove the nylon rollers from the regulator assembly/window. Prop the window up to about 1-2" lower than full up. Loosen the vent window frame bolts and pull the vent widow forward. Place a putty knife at the back outer edge of the window (slide it between the window and the felt on the outer side until you hit the uplock louver). Pull the window slightly outward and push the putty knife just past the uplock louver. Now pull up sharply on the window and it will come out without damaging or having to remove the felt. Reverse the process using the putty knife when reinstalling the main glass and frame. Note: the putty knife provides a glide for the uplock louver and allows it to slide past the felt without catching it.