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I had my sunroof lose calibration causing a leak. It wouldn't fully close flush, leaving about a 1/8" gap. I went through a automatic carwash and it completely soaked the interior. Had a 99 grand cherokee do the same thing but it was because of the windshield not being sealed correctly.

Check under your front carpet area for water. I had water under there as well. If it doesn't dry out, it could cause serious rust issues in your floor pan later on. Use a vacuum to suck the water out of the carpet and underneath it, then use a heater to dry it out. to check your sunroof, open it fully and look at the drain holes on the top side (should be towards the front). If you don't see anything blocking them (dirt etc). Try a small cup of water and poor it into the drain slots on each side. If it comes out the bottom of the jeep, it's not the drain holes that are clogged. It's something else causing the issue.

As far as going to the dealer, IMO I wouldn't. They would charge you an arm or leg to fix the windshield. I would take it to a windshield/window replacement company and see what they say first. They might be able to find the source of the leak and seal it back up for you for half the cost. That's what I had to do with my 99.
 
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