This is the kind of question that doesn't let me get any sleep at night. I looked at all the Fisher Body Manuals and the window handle looks like it faces straight forward or slightly downward with the glass up. I checked some of my unrestored GTO photos I gathered from the internet and some have it placed that way but others do not. Many photos show the cars with the glass down and there is tolerance from the window stops and placement of the weatherstripping. I looked at a
youtube video taken from a super 8 film when the cars were new and the '66 green car 36 seconds into the movie shows the passenger side handle almost in the horizontal position with the glass down. If I compare that to how I set up my crank, the glass up position is at 7 O'clock. Perhaps some other members will have better results.