On my '06 Limited we had the same water problem. Turned out, when you looked at the truck from above (standing on my deck was the perfect way to see it) the gap at the top of the passenger's door was extremely wider than the gap on the drivers door. Paid a local shop 50 bucks and it was fixed. They just had to align the door which got the seal tight and stopped the leak completely.
Not a bad trade off in the end when you think about what is over on the right side of the truck, computer, airbag, amps, heater box and so on and so on. Alot of things to protect from water over there.
Good luck with it.