Sadly, I just pulled A window out of my 95 YJ hard top.
I put the jeep on its side about a week ago. No Damage to me, little damage to the Jeep, but the Hardtop ripped itself loss and folded itself up.
The bolts ripped out of the fiberglass, and the top folded itself up. If it had stayed on the jeep there would have been no damage other then a broken window.
Ok, whining over. I pulled the remaining good side window using only a Dull Swiss Army Knife. Took about 10 minutes total. Here is what I did.
1. Cut lose the trim around the outside. This a T shaped piece of plastic/rubber around the edge. The top of the T faces out, while the leg fits in to a gap filled with sealant between the edge of the glass and the top. I cut the leg off the T to remove the top.
2. From the inside I ran the knife around the window parallel to the glass on 3 sides. It took multiple passes to get all the way through the rubber sealant. The corners took more work then the straight sections. After cutting through the rubber the knife tip passed through to the outside. I then tipped out the window and cut the 4th side. And the window was out.
When you get the knife between the Glass and the frame it is tempting to use it pry. Don't!
If you want to push the window out, do so with the palm of your hand this spreads the force. Prying puts a point stress on the edge of the glass and will cause it to break or Crack. If I had a dollar for every window I almost had out and pried on and broke.