I see by your post, you've started skinning the windows already. But here's my thoughts and actions on my own bus. This was on a Ward body bus. I know there are different configurations.
I went with 20ga. 4x10 sheets. Cut them in half. Primed on both sides.
When I mounted them (starting at back) the top went under the rain gutter. On the bottom, I removed at the top rivets in the rail and pried the top away for enough gap to slide the sheet metal between the rail and the body. With the metal in, it dropped down to the bottom of the rail (approx. 3") this gave me enought room to slide the top under the rain gutter. (left the rain gutter rivets in)
From the inside, I used RV caulking on the posts where the original window were screwed to. On the outside, I caulked under the rain gutter.
Using vise grips, I pulled the sheet metal to the top, under the gutter. With the sheet metal held by vise grips, I applied 2 rivets to the center of each post. Then re-drilled the rail holes and re-riveted the rail, leaving the last several inches free for the next sheet of metal. I then went inside the bus and drilled holes in the top of the metal, into the rail gutter and riveted those. Then moved on to the next sheet. I over lapped the metal by 4", with the foreward section on top. After one complete side was done, I went back and drilled all the vertical posts and applied rivets on 3" centers. After all that was done, I caulked aroung the entire window frame from the inside.
Thats how I did it , right or wrong.
As far as structural integrity in the windows, I would say there is none. Aluminum frames, glass and a couple of screws don't provide any integrity. I would say it's all in the posts the windows were screwed to, and that top rail section on the outside.
Sumbody stop me!