Jim,
Thanks for your comment. It's easy to overlook the fact that there will be people beyond the OP benefiting from threads like these. We appreciate it when you let us know that our advice is helpful.
I want to add two more points to what I've already written.
First, sacrificial plates with arrays of tapped holes aren't just for the faceplate. I have them for my faceplate, the rotary table and a small square one attached to a block that clamps in the MM vise. Making one for the MM table is a good idea but I haven't gotten around to doing that yet.
Second, in my method 2.2 I glossed over the business of centering the flywheel on the faceplate. With a rough casting, by definition there are no precision surfaces on which to apply a DI. What I've done in the past is to machine a bit of scrap with a hole that fits over the flywheel hub. Normally, the hub has a draft angle because of the casting process so size the hole such that it interferes about halfway down the hub. On the other end of this scrap turn a diameter that will fit in the tailstock chuck.
Mount the flywheel on the faceplate with the clamps loosened so the wheel can be pushed around by hand. Now bring up the tailstock with the fixture and use it to push the flywheel into a "centered" position. Tighten the clamps and you're good to go. This procedure accomplishes the "averaging" I referred to in my first post without a lot of faffing about. (Obviously, the fixture is removed before machining begins.)