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I actually like the blue stock ones, blue motors make me happy. It is like how Chryslers should be orange and Chevys should be motor swapped for something else ;D Plus the Powered by Ford reminds me of racecars in the old days.
I had a local shop paint them by hand. I probably could have done it myself just as easilly. While they get warm they are just covers and I think any black paint would work fine. If you are going to paint the whole cover I'd buy the ones from a GT and not paint the Boss covers because the Boss covers are almost twice as expensive.