Header Leak??

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ceramic....

Then I doubt they were overheated and warped the flange. Most coatings are good for at least 1,200F. If they got hot enough to warp the flange, the coating would have been burned and turned chalk white nearest it and for the first few inches or so down the primary tubes. This is usually result of a timing issue....generally and engine running with the timing too far retarded.
 
The problem in correcting it via this method, lies in the thickness of the flange. Having it plained for trueness might cure the issue initially, but you've now got replaced a flage that was previously very susceptible to warpage, with one that's even more susceptible. Since the metal is thin and there are no dowels to keep it in place, the header flange tends to move around with each heating and cooling cycle, which adds to the problem.

Your best defence against dealing with warpage is even torque across the entire flange.

The BBK's have a fairly thick flange, so my guess is that they're still probably pretty straight. The combination of a good gasket, high temp copper silicone and even torque should sort it out. I'd save any modifications to the flange as a last resort.
Every understandable, how ever that was my last resort with the BBK's on my mustang. First, I replaced the gasket with one of the Fel-Pro deals (paper), two months later the header gasket blew. The second time, I spent the money and bought the metal gasket, used the Copper spray and torqued the heads from the inside out with my torque wrench. From that point on, the gasket blew twice more using the method you previously stated. At this point in life I could replaced a header gasket in an hour. Needless to say, have the flange trued, paid the money for a proper gasket along with copper spray and torquing from the inside to out, I've yet to have a problem.

Just speaking from personal experience, replacing the header gaskets four times is a pain. I would hate to have someone go down the same path I did. Like you stated, the BBK's are thick enough at the flange.

If I were the OP I would try one time with the sequence Gearbanger 101 has stated. If that fails I would have the flange trued.
 
I used the high heat copper silicone in a tube, not the spray. I spread it around the ports with my finger to create the high spots specifically around them not all over the surface of the gasket.

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