I have the same exact problem with the front passenger window on my 300E, at any speeds above 65 it will make a whistling noise that will drive you crazy. I just crack the window and it goes away.

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Adam,
2003 Volkswagen Golf GL 24,000 miles. 1.9L I-4 TDI 5spd.

1986 300E. 115,000+ miles. 3.0L I-6 1st daily ride, around town only. (Gone)