Double check the taper for flaws, rust, scoring, etc. Examine the shanks for bright/burnished spots that are indicative of a bump in the taper. If you have actual tool runout, then there must be some kind of fault like this in the taper.
Do the limbo and get a bright light in there to examine the taper with. With a nice straight stone, hone away the bumps around any dents. Lay the stone in the taper, and swipe around over the dent while moving the stone up and down a 1/2 inch. Let the stone 'find' the burr around the dent.
If the taper has general rust, then use a fine grit emery cloth wrapped around a nice straight wooden dowel. Split the dowel down 1" from the end with a hacksaw cut, and slide the end of the emery cloth into the saw slot. Then wrap the cloth evenly around the dowel in barber pole fashion. The other end of the cloth you hold down to the dowel with a finger tip, the same one that applies pressure to the dowel. Keep it flat. Use a dowel large enough in diameter that it will not get stuck in the retention knob retainer. Run the spindle at 400 to 500 rpm and gingerly polish the taper. Keep in mind that you want nice even polishing from top to bottom, so don't carelessly overwork one area. Work it all as evenly as you can.
Then call Walt
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)