Be aware that if you remove the tracks from the roof - there is a set of gaskets between the screw holes and the the roof top. These gaskets are no longer available per the dealer. I used some rubber washers from Lowes and silicon rubber
I used Rustoleum high performance enamel spray paint. It's the taller , silver cans at Lowes. Did my rack and spoiler, and my wife's rack. It's held up great a year later. Sand any loose or flaking paint, the a coat of primer. Three light oats of black and you're good to go.
I didn't have any gaskets on ours. When I reattached, I dropped some silicone in the holes before I screwed them ack in. No leaks!
Professional High Performance Enamel Spray Product Page
do you happen to have any photos of exactly what you used?
Lowes has a selection of odd bolts, screws washers etc... They are all in slide out drawers. I found rubber washers about 3/4" diameter with a hole of about 1/2". Imagine a washer for the garden hose, but about 1/3 the thickness and about 75% of the size. I glued them to the bottom of the metal frame with silicon rubber and then coated the side of the washer that would rest on the roof with the same. Also ran a bead around the screw to make sure water didn't get in the screw holes.