Search the forums. I recall other owners citing leaks in the around the driver's door and the cause was a problem with the rubber weather stripping. It was a defect known to Toyota and repaired under warranty.
Most likely its the seams on the roof panel pull the 1st roof rack cover and molding and reseal the seam with silicone,I had a leak I chased and this YT video led me to finding it . FJ Cruiser ROOF LEAK Repair