Water Leak - Driver Floodboard Soaked

Was working on the truck today and pulled my all weather mats and door trim off, carpet is soaked beneath the driver side mat and also saw some moisture underneath both trim pieces for the door sills. Pulled the B-pillar off and didn't see any moisture so I ran a hose with wife in the truck and it started dripping out of the A-pillar at the grab handle. After pulling the A-pillar off and trying again, it looks like it's coming from the top corner of the windshield. I do have the factory roof rack installed, noticed a bit of a gap between the rubber of the windshield seal and the roof rack but passenger side seems to be about the same and so far haven't noticed any leaking on that side.

Think it's the roof rack itself or should I look at the windshield first? Losing daylight so I will probably park it under cover and run a dehumidifier tonight.

 

Seal between rack and windshield:


Leaking in the corner along the windshield seam, headliner doesn't appear wet:

 

You could try this..

 

Wonder if that's pretty similar to marine goop, but I think that's the plan after reading through other threads. I've been thinking about removing or replacing that rack for years since I've only used it for the tie down points when I have my kayak on the cap.

 

I pulled the roof rack off this weekend, good bit of dirt and some dead bugs under the rack so I'm sure water was getting in there, would probably only take one unsealed bolt to allow it into the cab. Weird that my headliner never got wet, maybe the water could just run along the pillar and out the grab handle without that happening. Planning to plug up the holes from the rack with allen bolts, dab of silicone on top, and then flexseal over the length of the gutter. Will also dab some windshield sealant in both corners of the windshield seal for good measure and test again.