Thanks for the 'links.' I hadn't seen LandCruiserSteve's sleeping platform/box yet, but it is similar to what I had in mind. A lot of backcountry skiers and snowboarders that I know have similar sleeping platforms in their pickup trucks. I made sure that the idea was feasable for the FJ before I bought it. Steve has a lot of good ideas that I will likely incorporate, although some of my needs are different.
Your dom mounts look pretty cool. Definitely beyond my machining capabilities. I guess necessity is the mother of invention in my case...
I think I will go back and silicone my adaptors. I didn't bother because it seemed like Toyota hadn't worked too hard to seal anything up there. But after seeing your comments I remembered that the black springy thingy under the bolts had some kind of gasket seal under it.
