Hi, congrats with new top, i had same issue as you with water leak from plastic window and musty smell from carpets, changed to new top and now no leaks.
If you had this problem over long time i've would check under the footrest carpet for any moist or maybe rust wich have developed over long period.
check this thread:
http://986forum.com/forums/general-discussions/36755-interior-water-leak-problem.html
986 Boxster
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