I ran the bolts between the intake and exhaust manifold hard finger tight, (no shim between the manifolds) then used a straightedge to line up the average of the exhaust and intake openings, moving the intake manifold to get the best alignment
Then I tightened the bolts gradually in several stages to "gut feeling tight" while re-checking the alignment of the holes.
Then I checked the flatness of the intake and exhaust faces using a flat surface stone, and of course, they did not align.
At this stage the purist solution would be to use a professional surface grinding machine.
However, I simply taped a large piece of emery cloth (180 grit i think) to the flat surface stone and sanded the whole manifold face assembly until all areas around the intake / exhaust openings had been touched by the emery cloth. You need to take great care that you press the manifold assembly face evenly against the emery cloth, and that you keep away from where the tape fastens the emery cloth to the flat surface.
This brought my assembly flatness below 5/1000.
It is probably easier to hold the assembly evenly against the surface while sanding if the exhaust ports stick further out than the intakes (like in my case) If the intake ports stick out beyond the exhaust, you may want to give the intake a go on the cloth alone before proceeding with the assembly
Now lets hope that your block is straight !