I've been trying to track down this information recently. I have a rack bolted on to the roof and wonder what sort of weight the fiberglass can safely take.
I had a 1st Gen 4Runner for 17 years, and considered mounting a rack the way you did (drill and mount directly).
It would be easy to build internal support hoops (like mini roll bars), with mounting plates attached, that your current mounts would bolt through (trapping the roof between the plates and the roof rack mounts). The feet of the hoops would mount to the top rail of the bed, where the canopy attaches to the body. This will transfer the roof load down to the metal body.
I would add at least one more tube, between the two hoops, to stabalize the system.
Another option would be to make the hoops stout enough for a roll cage, attach them to the floor, and remove the factory roll bar.
Review the interior cages (rear) at
4Xinnovations for ideas.