Thank you all for the help! All went smoothly.
Taking off the factory rack was very easy. I cleaned off the area once that was off. I cleared out the threads fairly well of old loctite. Put a big dollop of silicone on all holes and then placed the spacers on top. I mounted everything individually instead of assembling it all and then placing on top of the 4Runner. I was afraid I would scratch something. Bolted everything down and it all looks great.
For some reason i didn't realize the moonroof went into the body and headliner so I have full use of that still.
The rack is very quiet on the highway, I did not notice any difference from the factory rack. I did order the edge trim and did not check out the different with or without. Definitely works with it though.