Hi David,
My method (not necessarily the best in all cases - every situation has its own issues - some wheels will have eccentrics and cranks cast in)
1) Use a file to "fettle" the casting to remove all the flash
2) If both sides of the central boss (hub) need to be machined, chuck up the wheel and skim one side of the boss (usually only one side needs machining and the other cleaned by file and emery cloth so this step is unnecessary)
3) If possible, mount wheel in the four-jaw using inside jaws so the outer rim is clear, front, back and periphery (see first pic below) If this is not possible, mount on a faceplate (see second pic). Either way, you will probably need to use packing to prevent distortion and to make the wheel run flat and true. Set the outer rim of the flywheel to run true to the centre of rotation
3) Face the front and back (pic three) of the rim. If you really have to, skim the periphery, but it is usual to leave this unmachined and just cleaned up with a file
4) Face the boss and centre drill, then drill and ream (or bore) the hole for the shaft
It is usual to leave the outer peripheral surface of the boss unmachined
NOTE: The pictures are not mine - they are shamelessly copied from a couple of books by Tubal Cain
Hope this helps,
Ian