Making a dent in the header for clearance defeats the purpose of a performance header, if it don't fit that's IPD's fault, returnit or have them pay for mods. As far as the flange is concerned, make your measures then just take the pieces to a local small muffler place and asked them to do any welding/fitting (usually the chains won't do this). This is alot cheaper and allows you that nice "I fixed it good by myself" feeling.