Yes, cut the studs, but used 1in square aluminum bar screwed into studs to frame window They used Z channel for studs in the CT, so bars screwed in under lip on one side and used L brackets on the other. When the window screws in, it all ties in very strong. Of course, when the plywood gets all screwed in around the window also, it is even more solid.
This is a good way to do it if you do not weld or have access to one. Here's how it looked before closing it up. I had P hat type studs in my CTC so I did it very similar except there is an edge on each side to screw into so no L brackets needed.
If you have a welder and have the skills to use it, you just would use 1 inch steel tube to weld in frame as needed.
This is what it looked like framed in: I am sure you can do this for your second window.
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