The short answer: clean and deburr your spindle, taper shanks, collet body, the collet and use high quality tooling. If it dials in true after that, and you still get runout when the machine is running, then balancing should take care of the problem. This is assuming that your spindle bearings are preloaded properly to remove unneccessary looseness.
Oh, and take your most accurate cuts at noon when the sun is overhead, so the gravitational attraction doesn't pull your cutter east or west
