I popped the rivets off the interior skin using an air hammer. If you use an attachement that is pointed like an awl and pop the center of the rivet, then use a chisel attachment to break the rivet.
I then ran my air hammer with the chisel attachment up between the metal frame of the windows and the posts on both sides and the windows pop right out. Sometimes you have to cut some caulking.
After cleaning up the caulk and grinding down to bare metal around the frame I tacked up some pre-cut sheet metal with caulk, then used a 60 ml syringe to extrude some JB weld around the perimeter inside and out. It holds it like a weld. Then I used some window caulk to caulk the inside and especially the tops under the rain shield where the JB weld couldn't go.