Definitely check the rear quarter window moulding!
I had leaks coming from 2 places when I first got this truck, and a lot of the rust in the back sheet metal was on the passenger side close to the wall. Had my girlfriend spray the car with a hose while I was inside, and water just ran down...
Do you have an antenna for satellite radio that enters via the rear door?
I had an issue with water intrusion in the cargo bay, and it came from 2 spots:
1) passenger quarter window seals.
2) antenna that went from roof, under the rear door seal, down the side of the door and under the rear...