OK, here is an update... When I lowered the top, I could see the water inside the rear quarter panel space, in the space right in front of the wheel-well. Its right under the rear quarter panel glass, deep down. There is a drain in there that was plugged. I just took a long plastic stick from the window blind, and was able to reach the bottom of the space and moved it around, immediately the water started to drain... When I have more time, I will remove the inner trim panel to reach the space by hands in order to remove the debris...
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'06 Mustang GT Convertible
5 Speed Manual
Front Strut Brace
50k miles
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