It is pretty common to have to deck cylinder bases on cases. You always have to do mis matched cases and most of the time matched cases need it to. Here is a pic of dialing in the surface.
Here is the fly cutter in action.
Sometimes on mis matched cases you have to bore the cylinder spigots out as well. It only took a .010 cut to get this case set up. You want to take out the absolute minimum amount of material in order to make the cylinder slip inot the hole.
Here is a pic of dialing in the oil pump surface. The motor mounts are perpendicular to this plane, and this is the first step when re surfacing motor mount pads.