When you say "runout", was that measured on a round bar held in the collet ?
I may have corrected it a different way ( not suitable for higher speed spindles, due to out-of-balance issues )
- do not alter outer machine taper that goes into the spindle
- with tool installed in the spindle, check trueness of taper that contacts the collet with dial indicator ( should be close to zero TIR )
- if not, consider using the current setup with a boring bar attached to the table to re-machine the collet taper. By design, it should be true to spindle
( collet may seat a little deeper, the only concern would be if the collet "bottoms out" when clamping the smallest diameter that that collet can use )
If an NC, program the spindle to do the taper
- if a manual mill, turn the head to put one side of the taper in a vertical plane ( & use the quill to lower the holder onto the boring tool )
( both methods, check & re-check taper accuracy....if not right, then, the collet will not clamp fully using the entire grip area onto the tool shank )