Ordering new windows for old house... Wall thickness?
The sanest thing is to order new construction flanged windows that are a bit smaller than the rough opening. Then you integrate the flange with the WRB that you're installing over the new sheathing (right?) and bob's your uncle. On the inside, you can cover up the lack of square-ness with new drywall or wood window boxes, shimmed to be square with the window, not the rough opening.

Since you're taking this house down to the studs and redoing the exterior sheathing, let me mention that you have a golden opportunity to add extra insulation outboard of the new sheathing. The marginal cost will be fairly low, especially if you're doing the work yourself and buy reclaimed foam.

Resources:


http://www.greenbuildingadvisor.com/blogs/dept/musings/how-install-rigid-foam-sheathing
http://www.greenbuildingadvisor.com/video-how-install-rigid-foam-insulation-outside-house
http://www.greenbuildingadvisor.com/blogs/dept/musings/calculating-minimum-thickness-rigid-foam-sheathing