For aluminum or vinyl windows, the industry standard for window installation is AAMA 2400-02 "Standard Practice for Installation of Windows with a Mounting Flange in Stud Frame Construction"
http://pro.milgard.com/_doc/products...ma-2400-02.pdf
Out here in production housing, the windows are set by the framer so from a sequencing standpoint, the widows are set and flashed first then the building wrap is installed by the stucco sub. You don't see too much Tyvek or other "house wraps" out here, it's still building paper. Regardless of sequence, you still need to make sure the lapping is done in a weatherboard fashion to insure any moisture is directed to the exterior of the wall rather than the wall cavity. The problem with pre-wrapping the wall is that you don't get your building paper/wrap over the head and jamb flashing like the AAMA standard requires (Figure 6 in the pdf).