I heard that these guys who make racks for the Hummers may be doing one for the FJ.
http://www.gobiusa.com/

I will have to call to confirm.
One thing though, they have a basket on the bottom, no way to wash your sheet metal if this is covering the roof.

 

Now out for the FJC

http://www.gobitoyota.com/

Two styles.
One low, one high

Not sure if I like the style of these though, but at least suppliers are jumping to the demand of the FJC.

 

I think they're pretty sweet, don't really know about the $2000 price tag though. Four times the price of the stock rack, hmmm maybe I'm just cheap. It probablly wouldn't be that hard to fab. something similar right?

 

That is way to much $$$, and you will be removing it from time to time to wax the roof.

I am still in touch with Yakima, and I called them again today.
I asked about just brackets that would bolt into the stock 6 places on the roof and then secure my Load Warrior, but the guy said it is still gonna take a crossbar system up there.
Then the basket will bracket up to the crossbars like it does now on my rig.