So, it seems that my roof is leaking from parts unknown. The water seems to accumulate above the plastic trim that surrounds the head liner. I can see the water mark and it drips onto the driver seat which sucks.
What are the odds that the water is seeping in from the screws that are used to mount the roof rack? I do not have the rack just the rails but I think there are 4 screws on either side. Any help on this would be appreciated. Thanks.

 

pop headliner out and investigate

 

Was hoping to avoid having to do that...

 

It could be leaking in from around the windshield and migrating back or it could be coming in through the roof rack screw holes as you suspect.
You could unscrew the track clean both the roof and track, run a bead of silicone along the track with a dab in the screw holes and see if that helps. Unfortunately the only way to see for sure would be to remove the roof liner and have a look. In any case you may want to do this anyways you probably have a nice mould colony growing up there.

 

do you have a sunroof? make sure the drain tubes at the 4 corners are clear. take compressed air to the 2 at the front corners (you should be able to see them with the sunroof open). the 2 rear ones will drain somewhere under the truck, but I'm not sure where

 

Don't have a sun roof and I don't suspect the windshield as the leak occurs when the rear is higher than the front. Guess I'll pull those screws clean em up and re-seal them. Seems like a bad design idea to me. I guess I'll have to drop the roof liner too to clean up.
Thanks for the input guys.