Proper order of operations for re-doing windows, stucco, and footing insulation
I think I've answered my own question:

I'm going to do the footing insulation first. This will increase the effective thickness of the footings and result in a metal flashing plate over the footing foam at the bottom of the existing walls (for drainage and termite control/visibility).

I can use that for the wall project by resting the wall's new foam insulation on top of it. I haven't decided whether to screw the foam directly over the stucco or remove it first (see Adding insulation to exterior wall; remove stucco cladding, or add on top of it?), but regardless,during that time I'll remove the windows, build plywood bucks to put in new ones over foam and flush with the new stucco cladding, and flash them like so:

http://www.buildingscience.com/documents/insights/bsi-067-stuck-on-you