I know this has been discussed in a few threads but I figured I would do a more detailed write-up for those that have never ventured down that path. So rather than some vague descriptions, here are the detailed steps on removing the 5th Generation Roof Rack. I had more detailed pictures to include throughout this thread, but it said I was limited to only 11 pictures. I originally had 18. Either way, hope it helps those with the questions.
1.) Order your parts: The following parts will be needed to accomplish the roof rack delete. You will need the following:
8pcs - Part# 90119-08C47 (roof bolts w/ rubber washers)
4pcs - Part# 63185-42020 (roof brackets w/ foam pads - TE already have this under the installed roof rack)
4pcs - Part# 75596-35030 (roof plastic covers)
2.) Plastic Cover Removal: You will notice by the picture that there are two tabs holding the cover in place. These tabs face outward away from the car. On the front covers, the tabs are 3" and 7" measuring from front corner of the cover to the back of the cover. First tab at 3" ....2nd tab at 7". (see picture - You can start with either side first. I started with the driver side).
3.) Cover Removal: All you need is a flathead screwdriver and a soft rag to pop these off. Carefully wedge the tip of the flathead between the cover and the rubber gasket that it sits on.
Put a rag over the car and slowly pry up the plastic cover.....you will hear it pop when the first tab is free. Move to the 7" mark and pry up/out the 2nd tab until you hear the pop sound. Once both tabs have been released, rotate the plastic cover back towards the roof of the car. This will expose the two bolts holding the roof rack in place.
4.) Use a Metric size 12 socket and unbolt the two bolts found under the cover. These are very tight at first and tough to turn as the factory put a type of red threadlocker on the bolt threads. Slowly loosen these and remove the two bolts under the front cover, and under the rear cover.
This is the difference between the stock bolt (long/silver) and the roof rack delete bolts (black).
5.) Remove entire driver's side roof rack. Once removed you will see this:
There will be some bits and pieces of sticky black foam. I used a rag and wiped around the area...just to make sure it was free of any debris. This is important as once you replace this empty hole with the new brackets, a new seal will be made. The black metal brakets have a foam pad at the bottom of each end to prevent any water from entering into the screw holes.
*Note: You might want to put a bit of silicone around the base of these white tubes...just for good measure. The bracket foam pads paired with the rubber washers should do a good job of keeping any water out, but a little extra wouldn't hurt.
6.) Metal Brackets: Now its time to place the new metal brackets in their place. You will notice a little "arrow" imprinted in the bracket. I kept the arrow pointing outward toward the outside of the car. Now anyone can correct me on this as I do not have the repair/service manual, but I believe the arrows should point outward away from the car as this was the position that seemed to fit best.
7.) Install new Bolts: Once you have the new metal brackets in place, its now time to install the new bolts. I used a bit of blue medium strenght threadlocker on the end of each bolt to make sure it does not come loose. At the same time it should prevent any moisture from entering through the threads. Some people use build-a-gasket or teflon paste. Your choice. But the combination of the foam pads on the metal brackets and the rubber around the new bolt washer should prevent any water from entering. Use a metric size 11 socket to tighten these bolts in place (These bolt heads are a bit smaller than the stock silver ones. I can't remember the exact size...I'm pretty sure its metric size 11..... its one or two sizes smaller than the stock bolt). I'm not sure how tight they have to be, but usually my motto of "Tight is tight enough" should suffice.
8.) Install Plastic Clip/Covers: Finally, install the plastic covers. These have arrows molded into them as well. Again, not sure exactly which direction they should go, but I installed them with the side arrow pointing outward away from the car. They seem to fit perfect that way.
THATS IT! Your done. Drink a beer and enjoy the clean look of the rackless 4Runner.