John,
When machining a casting, machine the largest surface first and make sure everything cleans up before moving on to the smaller features. Also make sure the casting is centered. In other words, don't take a bunch of material off one side only to find out that there's nothing left to machine the features on the other side. On the other hand, don't just clean up one surface and assume the rest will clean up. You may need to take more off the face of the flywheel for instance, to get the face of the hub to clean up as well. Check all the surfaces to be certain there will be material left before cutting anything. Depending on the quality of your casting, there may be tons of stock everywhere, or it may be a challenge get everything to clean up. Just take your time and don't machine anything until you are sure. It's easy (and fun) to remove material, but pretty darned hard to put it back on! :banghead:
For your flywheel, try to grab it on the hub so you can access both sides and be sure that it's running true. An easy way to get it running true is to touch each side with a piece of springy wire as it turns, kind of like truing a bicycle wheel. Then machine as much as you can in that set-up (face, outer diameter, bore, etc.), flip it around in the chuck or re-mount it on a mandrel and machine the other side. Once you get some of it machined, then you can use an indicator to get it running dead on.
Tom