My 4 dr Tracker didnt come with a roof rack, so I bought one from a wrecker on Ebay.  Money well spent ($700 rack from the dealership, $59.49 on ebay, used).

Anyhow, the bodyshop is very strongly advising me against installing it.  They tell me that if the drill through the roof to mount the thing, the roof will rust.  Despite silicone, and rubber nuts and rust resistant paint, they insist it will rust.

The truck is only a year old.  I plan on keeping it for many years and I don't want to do anything stupid.  If anyone has had their roof rust from the factory installed (or aftermarket) roof rack, please let me know.  I just need help making the decision whether to tell the body shop (my cousin's place) to JUST DO IT...or whether to take their advice and leave well enough alone.

Well I would do it. Seems your precautions are the best ones. anythign can rust, but if you do this right I wouldn't be worried about it.

They told me the same thing about adding an aftermarket passenger side mirror on my lod Toyota truck. Had the truck for 200K and it never rusted.

Mark your holes for mounts and drill them out. Take a GOOD primer/sealer and swab the edges of the drilled holes and allow to completely dry. Then paint onvr the primer (most primers will asorb moisture if not painted over to seal it up. Allow the paint to completely dry. Then and only then add the mounting brackets being carefull not to over tighten or strip out the primer/paint in the holes you drilled.

Zig

I appreciate the note about the mirror on the Toyota.  

To the best of my knowledge, I am installing this rack exactly the way they would at the factory.  My interest is if others driving similar vehicles have had rusting or leaking problems.  My spare vehicle is a 1992 Suzuki Sidekick, but its a convertible, so I have no experience from that one to work from.

Did YOUR factory roof rack cause rust on the roof?  

I have a stock roof rack on my 4-door. It's rusted on each of the big tabs that keep it locked in and I have no rust on top of my roof. Even under the tabs. I have nightmares about rust, but its all chemistry so you can get rust anywhere if the conditions are right. Do what Zig says and you'll be fine! Make sure its sealed nice and enjoy the rack.

steveo

maybe I'll take a few pictures for you to ease your mind.

The "99+ trucks have a different mounting system for the factory roof racks than the pre "99 trucks. The old body style trucks used a clamping system to secure the rack the new body style uses bolts.