The block will be on its front face on blocks (timing cover face) so gravity ought to prevent crank walking. But I will check for crank runout 1st as a very good suggestion... this one is a new cast stroker crank, and has .001" total runout in the #3 main, so it might have a bit in the flange. As an observation, any runout in the crank flange could translate to many times that at the bell housing face, so the crank flange runout seems pretty important to know here. But the OP reports getting consistent results with the dial indicator turned at various angles on the flange, so he seems to have eliminated that part.
So what do you do with a machinist (or anyone for that matter) when you walk in with a well-organized, easy-to-read printed sheet with detailed and carefully taken data, and the first thing he says "I'm not even going to look at your data". (That's what actually happened in my 'sloped deck' incident.....) I guess ultimately the right answer is to go elsewhere.
