Was the original manifold tight to get off? You'll probably find your manifolds are warped slightly. I had 4 manis in my spare parts pile. 2 of them wouldn't fit when i tried them.
If replacing the studs doesn't fix the problem, you could try enlarging the bolt holes that require it as a quick fix and hope it bolts down good and doesn't leak.
When i had asked an engineer at work about machining the face of the mani, he didn't recommend it and suggested heating it up and straightening it was the best solution, obviously requires special equipment. I ended up just binning it and using a good spare.
Another thing you can try is removing the studs that are fouling, put the mani on and see if you can thread the studs in from the outside. If that doesn't work, at least you'll see how far out the holes are and how much to relieve.