Modifying A Bunkhouse

So long as you don't have any "systems" stuff in the way of where you want to open things up (plumbing, ductwork, furnace, structural framing, etc.), I think what you're describing is more or less doable. The windows may be somewhat in the way (and blocking them off would make the room rather dungeon-like, I think). There would be a fair bit of work involved, of course.

In what way does your daughter need her own space? Might the bunk as it is, with the curtain closed, be sufficient? Maybe try that way first and if things are not working out at all you can figure out some renovations.