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I have 2005 mustang and had the same problem 4 yrs after I bought my .Mustang when it was still under the warranty I took it to the dealer where I purchased vehicle.They charged me $150.00 to change the cabin air filter they said the old one was blocked with leaves and suggested not to park vehicle under trees which is kind of hard to do when I live on a street with a lot of trees. Everything was fine until 2 years later it started leaking in passenger side again.Pulled cabin air filter saw no leaves.Of course now warranty ran out .I went on a mustang web forum to find there were other people with same problem and not just a mustang problem there were other makes and models having same problems .One person fixed the problem. Here is the fix. Pop your hood look under where the cowl grill sits on the right and left side there is a rubber drain on each side( hard to see)so feel with your fingers check to see if they are blocked with dirt or leaves if so clean them so water can flow through them when it rains .That is what was causing water to come in on my passenger side right underneath the glove box in my mustang now every few months I check to see if they are blocked I have not had anymore problems with water coming in on passenger side . Sad thing is when i purchased my mustang i wish the dealer would have told me not to park my car under trees so i wouldn\'t have a water I would have thought twice about buying a car that you can\'t park under trees because I live in an area where there is a whole lot of trees.Thanks a lot Ford for designing such a crappy car !!!! Good luck I hope this fixes your water problem.