Ok now I can see the beast. I would mount it on the mill table with the flange faces down and see where it touches. Bolt it down at the contact points try not to distort it, place shims under high spots. Now mill 2 or 3 flat s[pots on the ridge at the back. They need to be large enough for positioning on 123 blocks or similar, or maybe machinist jacks.
Now flip the part and set up on blocks or jacks on the flat spots you have created, securely clamp the manifold down and you should be able to lightly mill the flange faces true and square, taking only the minimum off that you have to to get a new surface. Job done.