I have a JDM 4-1 on my car and the flange is starting to rust. I plan on taking the header off while I am redoing my suspensions, gutting my A/C, and swapping in brakes. What can I do to stop the rust, and has anyone else had this problem?

 

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My DC header's flange started rusting the next day after it rained. I'm not sure what you can about removing the surface rust, but I never cared to do anything about it.

 

You could use a dremel tool and some polishing pads to polish the rust off and then spray the header with high temp engine enamel.... aluminum colored would compliment your engine bay quite nicely. Spray the entire header though, not just a spot here and there. Be sure not to scratch the paint while installing it or after installation or it will just rust again. good luck