Just FYI - I have had my roof rack off a couple of times and the "gaskets" under the feet of the rack do not seal it much at all. In fact the roof gutters run directly under the front feet on my '00 so there is actually a small gap under the center. The gaskets are made of a fairly hard plastic and moisture can get under them. Also, if you do run the wires down the tubes you might have to split the harness to get around the little threaded insert that holds the foot in place. Any hole you drill in the roof ought to be sealed and rustproofed independently of the gasket and foot - maybe you should consider running the wiring harness up from the interior and installing an extra inline connector (depending on how many conductors are in the harness) so you can do the wiring in the roof rack independently and then make the connection as you're reinstalling the rack, stuffing the wiring and connector up into the foot before screwing it back to the roof. You will see when you disassemble it that there is not a lot of room to work with because of the way the thing is constructed. For the trouble this might end up being, you might want to think about just running the harness outside of the legs and drilling a roof hole just inboard of one of the feet so you can seal it properly. You could probably find a decent watertight aircraft-type connector that you could mount flush right into the roof so you could remove the light bar occasionally without worrying about plugging holes. Good luck with it!
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"It's always something..."
R. Roseannadanna