Hey Dave,
As you get down in the tolerances the whole system comes into play. If It's big variations then maybe there is one culprit to be found causing a problem. But when you start cutting hairs sometimes it's difficult to refine the machine
/ system and frankly may be wasting your time.
Here is an example:
My old mill, which I CNC'd, will produce an egged hole when milling a circle to hold a bearing. The gain in the lead screw is 0.00025" / inch and that gain varies over a 12", but there a few sweet spots in it's travel, the ball screw is within spec. I can use the sweet spot, even adjust the steps, and do an extra step or two and produce a very close tolerenced hole which is not egg shaped if i want to take the time to do so.
My engraving machine is different in that the X & Y have phenomenal accuracy and the Z movement is great also.
So no need to even think about tweaks, but, the tool runout can become limiting.
So there's were i come from in my response and logical to me ( FWTW ).
RICH