I don't like ca for photo etch, there is no time for fitting. I did the same but with watered down Gorilla glue.yeah, especially increasing the size of the openings so that they fit properly. And then there are the opening that are already too large! The wax pencil idea I got here for picking up and placing the windows was a life saver. Are you using CA glue? I use Elmer's white glue that has been watered down slightly. I allows you to move the part around to get it just where you want it. I'm not sure of the pros/cons of using CA. Maybe I am missing a better way of doing it.
About Gorilla glue, the producer .has ceased production so if you like it, stock up!