You will never get those windows to look 100% baz1701 .
The reason is that you are adding in allot of verts to a curved surface with so few polygons, you can cut it in all day and tidy up, but it would not look allot better than the way you have it now. (currently looking good IMHO)
I would, select faces and tesselate them by edge. this triangulates each poly for you, so when you cut windows in it helps. try to expand the cuts outward toward the hull also, dont restrict the folds from the windows to a small area as you will have those shaded anomolies as max tries to fold your smoothing groups.
good luck.