You've done a lot of trial and error testing, so this may lead nowhere. But my thought is what babymog said below: a slightly cocked driver side window. Try this. Run the window up all the way closed. Then lightly tap the window switch down just enough to unseat the glass, but not to move it down at all. That would be just enough to un-cock it in the guide rails and align it properly. Could be the answer.

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1988 California version 260E (W124)
Anthracite Grey/Palomino
Owned since new and still going strong and smooth
MBCA member

Past Mercedes-Benz:
1986 190E Baby Benz
1967 230 Inherited from mom when she downsized
1959 220S Introduced me to the joys of keepin' 'em goin'

There are only 10 kinds of people in the world--those who understand binary and those who don't