Peco Header flange not sitting flat

I just installed a Peco exhaust system header to tailpipe and the front two flanges sit smoothly against the engine and have no problems, however, the back flange it having some problems... The top of the flange rests on the engine and there are no problems, however, the lower side of the flange is not flat and causes a leak. At first, I thought that maybe the intake manifold was too thick and therefore the bolts were not able to press all the way against the manifold flange so i had the intake manifold machined down. That didnt work. I then took the car over to a muffler shop thinking that maybe i had misaligned the system and that by tweeking it, they could get it to line up. They were unable to. So at this point I'm not really sure what to do . Any ideas??

Return it and get another. Peco did have quality control problems on their headers a couple years ago so it's possible that you got on left over from then.

The only other thing you can do is have it machined flat, but don't go too thin. You may want to machine the intake to match so you don't have to use spacers.