When I had my '85, I was thinking of making one that sat on top of the bed sides, like a lumber rack. However, it may be hard to get the removable top to seal...
I saw a custom one on a pickup (w/ camper shell) in Durango, CO, years ago that I thought was pretty cool, from a functional perspective.
The guy used tread plate on the top of the bed sides that extended out about 3" past the sides of the pickup, all along the sides. His camper shell sat on the 'inside' portion of the tread plate, and the rack uprights were welded to the 'outside' portion.
With the tread plate sticking out like that, it not only provided a place to weld the uprights for the rack, but it made a ledge he could walk around on while loading or unloading the rack. Plus it would serve as kind of a rub rail down the side of the vehicle.
Let me see if I can illustrate:
End view:
H C
----
...B
H is the uprights for the roof rack
C is the camper shell
--- is the treadplate
B is the pickup bed sides
.... are place holders to get things aligned properly. Pretend they aren't there
I don't know if the idea could be adapted to a 1st gen 4-runner, but I wanted to try...
Shoulda never sold that Toy.