Had another thought for you Jim, for when the radiator cools down....I get that one
It wouldn't hurt to mic around the flywheel, to check the actual height or thickness, width, you know.
I'd use this as a double check to look for clues. Just measure from the machined face to the back of the wheel, maybe do it every inch or 2 to start
A nice tenth indicating micrometer, not calipers is what I would try.
We have a guy who can also regrind the register area
Again, no way that you are getting crank shaft end play wandering in and out?
Wedge the wheel against the bellhousing ears on the block with a tapered hardwood block maybe , creat a slight drag as you turn the wheel,,,push the crank back, or at least deflect the assembly consistently as you measure with a big screwdriver, etc.
Now you measured the crank flange run out, did you use a big faced tenth indicating indicator?
I'd look close there, and stone the areas I discussed
One good burr can kick a flywheel out of true, no doubt
Nice work