This is how I waterproofed the installation of my Yakimadaptor. You could try this technique or if you are worried about water (or if you're in a wet climate) you could just coat everything liberaly with a silicone sealant. I chose this method so that the Yakimadaptors could be removable, but other people may not be worried about that.
First, the cover comes off by pushing it forward toward the front of the car. Sometimes the front edge pops right up, sometimes it's a struggle.
If you are removing the POS factory rack, be sure to
read this.
Unbolt the clip thingy with a 10 mm wrench. You might be interested in checking out Toyota's waterproofing. There is rubber on the bottom of the clip thingy and there is a rubber gasket under the bolt head. Now, get in there with a sponge and clean all the grit out of the gutter. Cleaner = waterproofer.
Drop the gasket in place...
Next I take some of this:
And I just smear a little film around the chamfer for the flathead screw.
Now crank down those flatheads.
You can see it forms a nice little bead. There's one on the inside, too. The gasket seal cleans up with alcohol, but otherwise it should pretty impervious. It'll form a skin after an hour and it'll be pretty rubbery in few days. You can read about it
right here.
.
This setup should keep water in the gutter from getting in the roof and it should prevent water from entering around the flathead screws. But if you are paranoid or if you live in a rainforest you may want to silicone seal cr@p out of everything.
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