I had same problem with my 2012 E350 4matic. After clearing sunroof drain holes,I still had the problem. It turned out to be the windshield sealant right along the top edge of glass. I masked off top edge of windshield glass and edge of car roof and tooled in Permatex Windshield Silicone Sealant. It is a more fluid,liquidy version of silicone. It flows into crevises. No more problems the past 5 years.
you can peel back the outer \"lip\" on the gasket type seal and use flowable silicone windshield seal (permatex makes it..). peel back the outer lip starting at the top and start to apply the silicone toward the sides and the bottom.. be very careful because this crap flows everywhere and is nasty.. so use it sparingly. i have used it on quite a few cars with great success. my wife's 81 leaked on the sides of the seal and i used the permatex product, and no more leak after that.
My 4runner was built in Japan and I most likely have a bad windshield seal that makes a horrible glass on metal noise as it gets colder.
That crusty rubber seal was the press-in seal - the biggest problem with the OE VW version is that it's more plastic than rubber and it shrinks in the sun.
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