Hi Randy,
The windows were so badly pitted that they ended up replacing them! We did try acid on a small area which did loosen the mortar like substance but the windows were pitted under the mortar.
Before trying anything, I called and went to a few window repair shops and they all said the same thing - the windows will need to be replaced if the damage is that bad. Other than the windows, the construction clean went very well.
Thanks, Anne