This was one of the more difficult Model A tasks we've done to date.
The specifications say a total runout of .006 taken at 3 points on the top 180 degrees of the flywheel (9 o'clock, 12 and 3) cover is ideal for proper clutch and transmission alignment.
Initially, we had big troubles getting to this tight specs. Until we figured out a system that that worked great and brought this assembly into proper tolerance.
Here's a great reference that explains more detail -https://fordbarn.com/forum/showthread.php?t=94270