I no longer have the Sport Edition roof rack on the 4runner but I still have the parts. It's actually very simple but you have to remove the mounts from the roof. There are a couple of washers that keep water from coming inside that you have to be aware of when you reassemble. For tools, you'll need a thin pry tool like a putty knife (I used a paint can opener), a T-40 torx bit and a smaller box bit (don't remember the size).
You will have to remove both the driver's and passenger side mount.
Start by locating the seem where the top cover meets the bottom cover.
Split the seem with the pry tool.
It may take a little effort to pry it up. Once you get enough of a gap you can use a large flat blade screwdriver (wrap the blade with tape so you don't damage the plastic cover) to pry it up the rest of the way. I was able to do the job with just the paint can opener.
Once the cover is off, you'll see two torx bolts. Remove those. There's also a small torx screw on the side of the mount where it connects with the rail. Remove that screw.
Place something under the rail (like a block of wood) to support them when you remove the mount. Once you remove the mounts on both sides, loosen the locking knobs on the cross members and slide them out the ends of the rails.
When reinstalling the mounts these are the washers I was referring to that keep water from getting in the cabin. Theres a paper washer between the top of the bolt and the mount. The there's a pliable, gummy washer between the bottom of the mount and the roof. You'll also notice the bolts have a green sealant on the threads. You can probably use silicone sealer to seal these areas.