I met with the Professional Engineer on the site today. The back wall on the top floor is an area of concern since it has so much window area. The plumber also had to cut out a substantial part of the studs to get plumbing through for the kitchen sink.
Carlton (the PE) was overall impressed with the quality of the framing--a comment I have heard from several professionals. His method of testing for strength on a wall was simple--he hit it HARD. Then he looked for areas that flexed. As suspected the back wall had a bit of flex--not enough to be dangerous.
To be safe we are going to have it reinforced with a L shaped steel channel on the outside during the masonry phase. That along with the masonry should make it quite stiff.