Check and see if there are any missing plugs in the floor (you'll have to physically look under the car for the round rubber plugs) or if there is a puddle or open hole from a missing plug under the spare tire. Another thing you can do is to check and see if the plastic moisture shield is still in place between the inside of the door panel and the door itslef (but...you'll have to take the door panel off, which will take 5-10 minutes. See what happens when you adjust your hatch, that also may be causing moisture to get in. Are there any wet spots on your floor when it rains?
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Mustang Parts Specialties ripped me off, it could happen to you as well.
'84 Mustang 5.0 LX
my LX
'89 Mustang GT
my GT