I too have been experiencing OOR and I decided to take some measurements to come up with the best solution.
With a dead drive inserted in the headstock I get a deviation of .0015 if the dead drive is inserted to give me the best reading. If not oriented properly the dead drive deviation can be as much as .005.
The adjustable mandrel gives a deviation of less than .001, again if it is inserted with the right orientation. With the mandrel saver set at about a pen blank's distance that end of the mandrel whips around at about .008.
The Beall collet chuck gives a deviation of .005 at the chuck with a quarter inch drill bit inserted. I don't understand this because the Beall collet chuck "should" provide less deviation.
Larry, after reading this thru several times it appears that you have a situation similar to mine.
I won't go into great detail but basically it comes down to marking the dead center to get the least amount of runout, called the 'sweet spot'.
In my case I have determined that the MT2 was bored off center and the dead center I have also has a slight off-axis cut. If positioned correctly, the runout on the tip of the dead center is just under .002" so that is what I deal with. I have used a small file and marked the headstock drive and the dead center so it is easily positioned correctly each time.
If you have a problem with runout on anything that threads onto the headstock, and there is a runout on the headstock itself, there isn't much you can do about it since you cannot easily change the position of the chuck on the threads.