Most manifolds have a flat spot along one edge of the holes at 90 degrees to the face. You can put it face down first and mill these flat spots. You don't need much, maybe 10 -15 thou. This gives you a perpendicular surface to flip it over and clamp to an angle plate. Way more rigid when milling.
This is a video of the head from a Red Seal continental. I had a video of the manifold but it says it’s too big a file to load. This is on a horizontal but a vertical mill is the same principal
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Martin W