Well, getting the base flat makes setting up on the mill table WAY easier. I'd suggest going until its flat enough to not rock.
I think I used a boring head for the cylinder (never went to the lathe for it) since I wanted to drill the bolt-circle at the same time. For the cylinder, I did:
Face the inboard side, bore the cylinder and drill/ream the valve, drill the bolt circle.
Flip, face the outboard side. Use the coax indicator to center for the head bolt-circle, and drill the bolt circle.
From there, the only ops left were to drill the holes through the valve, and the angled holes, which each had to be done individually.