Are you aligning the quarter windows to the body or to the door glass? Only reason I ask is one of my friends was working on his '67 Galaxie and had a similar problem, he couldn't get the quarter windows aligned with the door glass. After days of fighting it he asked an old body man for help. First thing he did was align the quarter window in the body ignoring the door glass and then aligned the door glass to the quarter window. My friend said it took the guy about 25 minutes per side.