I measured some runout on the shaft couplers.

Discovered I had made a mistake when modeling the D shaft and corrected it.

The new ones are printing.

EDIT: Nope.  This made it worse.  I rotated the part 180 degrees and printed again just to make sure it wasn't a calibration issue with my printer.  It wasn't.

I had the same result in both ABS and nylon.

I think the part is actually distorting when I push it on the shaft due to it being a tight press fit.  

The D shaft profile is "perfect" as designed with the flat removing 1/10th of the total diameter, but once I pressed onto an actual stepper, it warps the centerline towards the flat on the D (angularly, concentrically it's still basically perfect).  This results in my stepper wobbling about as I rotate the shaft.  I wouldn't care except that it as it does it, it also affects the line length.

I need a tight press fit here to maintain concentricity of the stepper to the spooling rod shaft, or I will need to either nix my vibration isolators or add another bearing.  I've built some pretty loud printers in the past, so the vibration isolators are staying.

I tried angling the D indentation slightly to see if that compensated to no avail.  I'm iterating now to see what else will correct this.

EDIT 2: Turns out my D shaft profile was fine.  

To give the AL rods some better grip when I glued them into the couplers, I had knurled the end with a pair of linesman pliers and wasn't consistent enough. When I turned the AL rod around to the smooth end which normally goes into the bearing, the wobble went away.  

Well at least I got a slightly refined shaft coupler out of this little exercise.

Saw this live when it came to Chicago back in the day..