EDIT 8/28/11: Found one! Mods, you can delete this thread if you want.
I'm not quite sure what this piece is called, but it covers the area where the stock roof rack would go. I am missing one. I am willing to buy one, or both (only need one though) for $20 shipped. I figured someone might have them lying around if they installed a stock roof rack.
This below picture with black piece of rubber on the roof is what I am talking about.