I was in there recently, as I was changing out the weatherstripping and inner/outer guides, and pulled off the cover to pound out a dent. It's really not too bad.
Pulling out the window is the thing you have to be careful with. You can bypass the safety switch so it will wind out when the tailgate is down and you can disconnect it from the regulator and pull it out. Be sure to support it so it doesn't crack or fall out. It is somewhat heavy.
It's really little different than a regular window, just on a larger scale, and you don't have quite as much room to work as you would on a door. My motor works so I didn't bother to replace it, but it looks fairly simple to remove. The access panel gives you reasonable room to work. My channels were okay so I just shot in a little silicone spray and the window seems to operate a little faster/smoother now.