I too had the same problem on my GFs car, an import not a mustang.
I bought it to AK Autoworks 604.688.6378 ask for Khang Manager, took some time but they traced it to where the slight gap was where the water seeped through.
The issue was near the antenna hole.
I had a 1999 mustang for a short period before and notice that oftentimes water go through the retractable arm area but unsure thats your problem.
Good luck with the search.
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