Trim Cuts along staircase with angled wall

Measure in a foot or so from one inside corner and make a mark. Then measure from the opposite corner to your mark. Add the two measurements together for the full length.

Note that this process is shown with pictures over on the blog.

I would case the windows too. No need to tear out the sheetrock if it's sound - nail right up over it to the framing wood behind it at the corners. What you use to do this and how exactly is up to you, the functions of the windows, and the wainscoting. The wainscoting is going to add visual bulk and interest to the surface of the otherwise blank wall, and leaving a window in the same room as it uncased is going to make the window look naked and unfinished. I might take it a step further and suggest adding crown molding to the room as well, for the ceiling-wall corners are also going to look naked and unfinished with the heavy wainscoting present in the room. Wainscoting is part of a larger system and method of finishing a room that I don't think it can be divorced from without sacrificing harmony.