@COYS the FSM shows the door card removed, but I don't see anything retaining the channel run that would necessitate it. For example, older Jeeps have a screw at the bottom of each side holding the rubber in place. It's been long enough since I replaced my rear channel runs that I don't...
@Francis K looking at it again with fewer beers in me, it really looks like the outer lip of the window channel run is completely missing.
The area circled in yellow looks like bare metal. The area circled in red is what both sides should look like.
I maintain that the edge of the glass...
No, I'm saying that the clunking was so bad that I didn't think you had them until I saw the rubber strips on either side.
Your window isn't attached properly. Either it's come out of the glass channel or, as others have said, the regulator assembly isn't screwed down. You shouldn't be able...
At first, I thought you didn't even have any window runs. I'm skeptical that your window is even seated in the glass channel (the thing that connects the glass to the regulator arm).
Pull your door card and plastic liner off and inspect. It's maybe a half hour job.