I thought some more about the driver’s window alignment problem and decided to take another look at it. While I was there I took some pictures. Here’s the inside of the door with the wire rope that controls the window position.

When I realized that one problem was that the top of the window needed to move forward when fully closed, I loosened the rear rope attachment point, pushed the window into position and re-tightened the attachment screw. Voila! The window now stays in the channel and closes reasonably well.