There is a bit more too it than has been discussed. Further help would require you being willing to disassemble the spindle and post pictures of the spindle parts (including both bearings (both sides of each). Lots of details are involved in assembly of a precision spindle.
It's good to read the spindle taper runout was very very little.
I'm pretty sure I've got the spindle assembled right. I'm not risking the bearings by removing them. The pictures above had the spindle in them.
I'm going to track down the motor vibration issues tomorrow and get a different v belt. My alignment wasn't the best so I'll fix that while I'm at it.
I think things will improve more in the morning.