Its pretty easy to do. Just need a strong nail to pop the cover off the roof rack end bracket. Once you remove the cover all the bolt are exposed. The middle come off after sliding the main rail off and exposing the 2 bolts inside.
Now I just need to find a cover to plug the hole temporarily until I finish the new rack design.
Mine was clean underneath. No trace of rust whatsoever. The bolt was sealed using clear silicone but I could see moisture getting trapped underneath the rubber booth. I might put a thin layer of clear silicone underneath when I put it back.
I am planning to build a full length roof plarform. I dont want basket type since it would prohibit me from parking inside the garage. This just for carrying lumber or ladder if I need something for the house and would be build to accept all Yakima acessories. More like the picture below. That it what I have in my old Montero. I am still looking for suitable adapter to mount it to the roof.
I recently looked into roof racks for my 99 100series, and purchased a yakima road warrior. Course its a basket and not what ya want. There are racks that will mount where the stock cross bars mount. Time and money made me go with the yakima. I am interested where you would mount a rack w/o the factory one on, would you fab up everything yourself?