Just a heads up for anybody about to remove their stock rack. Here's an issue I ran into yesterday when trying to remove the stock TRD Pro rack/basket.
The bolts are in there tight with red thread locker. Both bolts go through a metal bracket that sits on top of the roof, through the roof itself, and thread into another metal bracket with plastic tubes that floats inside the roof liner itself. Loosen both bolts FIRST and really make sure they are completely broken free from the thread locker and can almost be removed by hand BEFORE you actually remove either bolt. Why?
If you remove one bolt and then go to break the other one free, you risk breaking that floating bracket and it will just spin inside the roof. And you're screwed at that point. This happened on one of my brackets. I was able to stick a screw driver down into the hole and capture the floating bracket again. But by that point the bracket was FUBAR. Plastic tubes sheared off and the bracket had bent.
Toyota was NOT helpful. The service department didn't even want to look at it. I'm going to have to drop the headliner inside the SUV in order to get the bracket out and replace it with a new one.
The part in question is #12: