Don't rule out the trunk seal. Mine looked like new as well but it still had a couple leaks and when it rained I would see it. Crawl in there with a light and have someone pour water on it. You are likely to see it leaking in. I was a bit confused by the post but you put the window on the other car and that didn't fix the problem then it might have been a trunk seal too. This is the easy cheap option and only takes a couple mins. If you don't see a leak then I would look closer at the window. It is unlikely that if your last car was fixed and it still leaks that it was the window to begin with.

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76 300D 130K "Stella" (Sold )
74 240D 299K (Donated to Highschool For Senior Project WVO)
83 300TDT 290K (My one and only)
Sanford, NC