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Sometimes the passenger side window isnt fully closed...if thats not the case then it could also be leaking from where the door meets the roof like kind of where your pilar is...I remember my car used to do that and i had to take off the pilar and seal it..

If thats not the case then I'm not sure but the 3rp picture looks like it has something like a crack or maybe im not seeing right...Maybe someone else can chime in and give some opinions

 

check to see if the grommet between the door and chassis is in. like when you open your door look at the hinges and you will see a grommet around there. just make sure that's in. also if it rained that much maybe water came in through where the cabin air filter sits. If you remove your wiper arms and take the plastic cover off you might be able to get a look and if its really wet there then it might have leaked in.

 

oh yea nice good job if the water rose that high then maybe it did come through there.