It could be the little plastic track sliders,
Mine had the same problem minus the clunk and new sliders fixed it. You might want to take the panel off to peek around first but the sliders either way are probably worn. The rear door had problems going up and the slider was broken where the metal arm was pushing the window up...not pretty but a file, some grease and a new slider made it new.
95 E34 530I V2.37
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Those who make peaceful revolution impossible will make violent revolution inevitable.
John F. Kennedy