1 - Bad windshield seal
2 - drain tubes from the sunroof run down thru both A pillars. (could be stopped up or broken) You can check them by opening the sunroof, and pour a small amount of water into each drain hole in both front corners of the sunroof. You should see the water run out of the bottom of the truck just behind the front wheels if the tubes are clear.
3 - Check roof rack bolts. Have heard a few folks say they've had water get in around them also. New thread sealer on the bolts should be a quick fix for this.
4- Be sure to get the driver's side leak fixed asap. If water leaks down the A pillar, and onto the GEM module and/or the fuse box under the dash it could cause all sorts of problems/issues with the electrical systems in the truck. Lots of info on the internet about it if you search it.
My 2000 leaked at both handles on the A pillars right after I bought it. I had the windshield re-sealed and that fixed it. MOST of the time that fixes the issue of water running out the A pillars. A few months later I mysteriously had water come out both handles on the driver's side A and B pillars. That leak turned out to be a couple of tiny holes in the main drain track, on the roof, way in the back. That explained why it was so intermittent, and only leaked during long right hand turns during heavy rain. Boy was that fun to figure out!
