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I got the guys in the machine shop where I work to flatten the flanges with some wet and dry and a flat plate because I could visably see a bow in the flange face. I have never had any problems since.
Agree with Nez in getting the ends re-faced, particulary the turbo end.I had an original version H&S version on my old MY01 that wouldnt seal but after having it re-faced it was fine.