Since we're diving into "lessons learned" with manifolds, a couple of other hard-earned words of wisdom* to pass on:
1. When checking the manifolds for coplanar across the mating surfaces as Marshall shows in his first picture, I believe the general consensus is that up to 0.002" is acceptable gap.
2. After an intake/exhaust manifold assembly has been decked, either by using a mill or by sanding as NK suggests, it's important to check whether there is enough recess left in the manifold to still accommodate the glands (if you are going to use them). A simple dial micrometer can measure the depth. Also measure the depth of the recesses in your block, and add the two together. That should be equal to or only slightly less than (say 0.010") the width of the glands. If not, you can grind or sand down the glands.
3. How much "droop" is acceptable for the exhaust manifold? If you want to use the glands, virtually none. If you can forego the glands, then I've been successful getting a manifold with a bit less than 1/8" droop to seal properly. Any more than that...
*Wisdom is gained by experience. Experience is gained by making mistakes.