Not sure if they do with manual cranks - but the power windows do, I believe (most Cougar interior pictures I've seen seem to have the same power window switch set-ups as our cars - 5 switches on the driver door).
If you're wanting roll-up quarters, the regulators, brackets and hardware from coupes and 'verts will bolt right in to the fast backs. I just did mine this past weekend, and aside from still needing a bit of adjustment (to free up the action - they're tight) they work great!