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Chief - Hey man. For what it's worth I've been in 2 Mustangs with the window louvers. Actually 3 now with mine. None of them had the inside of the louvers painted. Mine came prepainted from Roush. I don't know what brand the others were or where they were painted.
On the other hand if you have gray paint fingerprints, that's cheese. I'd have them fix them as well. I wouldn't go through the hassle of painting them unless the color bothers you. They could just easily use some mineral spirits on the fingerprints.
WRXified, Thanks for letting me know that the louvers you have seen are black on the inside. That certainly helps. Maybe they can just remove the painted fingerprints. This is getting easier...
Hmmm, I guess someone couldn't figure out how to stick plastic side scoops on a car correctly when Ford put them on my vehicle. oh well.
Here is another picture - close-up - that shows the installation of the side scoop. I think it shows the 1/2 inch drop below the body line that runs through the door handle: http://www.mossmuscle.com/Shop/ViewP...eIndexID=82654