I'd talk to Winnebago about this directly. I'd be concerned about structural integrity if you put in your own window. I'm not sure Winnebago would do it, but it's worth talking with them to see about customizing the unit.
We've had a Winnebago bunk unit for 10 years, been a great unit as out kids grew up and we still take it with them even though they are in college. My only suggestion would be to look around at at used Sightseer 35J - one think I like about our is the space and not feeling like we're all on top of each other. I haven't seen your unit in person, but as I did the virtual tour it seemed tight. Just a thought.