Difficulty Rolling Rear Windows Up or Down....

I don't know about rear windows on these cars, but the fronts have a rubber stop at the bottom that limits the downward travel of the glass. If that is out of place, the glass will fall below the seals, and be tough to align back up.

Of course you did mention the rust removal. Is this an aside, or do you feel it's related? Perhaps the regulator channels are filled with scale. Do the windows roll up smoothly once you get by the seals?