Yeah, you are correct - DON'T use CA glue for windows, most often it cause a real mess with hazing and crazing.
You could use Testors or Model Master Clear Parts Cement & Window maker. They work fairly decently. They can even wick in between the clear window material and the structure. If you apply a little too much, it will still dry clear, but you will be able to see it if you look close. You will have to let the parts lay undisturbed for awhile to give the cement some time to dry.
I prefer to use a liquid model cement (or in my case, MEK thinner) for gluing in clear windows whenever possible. That means both the clear plastic and the opaque plastic substrate must be "meltable" (is that a word?
) by the cement/thinner. Some plastics are kinda' impervious to it, believe it or not. Fortunately, I know styrene plastic melts, and I believe acetate also melts with MEK or liquid model cement, providing an excellent bond.
Lay clear acetate over the window openings inside the structure, apply the liquid cement or MEK thinner with a fine pointed brush so it wicks in between the acetate and the plastic, then let it dry for a few to several minutes. Don't mess with the clear acetate until dry, or you most likely will be taking it out and trying again with a fresh piece.
Those are my favorite methods, and hopefully others will chime in with theirs.