I had to devise a means recently to perform a similar measurement (glass capillary with 1mm OD, 25mm length, 0.009mm perp spec runout at edge).
Utilized a high-end vision system, native lens resolution of 0.8um with 4x sub-pixel interpolation.
Collimated LED backlight (prime importance for this applicaton)
Precision Levine spindle/collet combination.
Autofocus on OD edge, define XY coordinate system based off of OD edge.
Rotate part 3-5 revolutions while using a point edge finder to track position of end face at the periphery and store data points (~100's) in an array.
Find P-P excursion of edge points with respect to X to yield end face runout.
Achieved sub-micron repeatability and accuracy.
You may also want to look at the TM-006 from Keyence, In-Line 2D Measurement Sensor.
Whatever means you use to rotate the part using such methods, you must minimize axial runout, wobble, and ensure coaxiality to your measurement axis.
-AK2DM
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