Found something that works. Y'all tell me if I am screwing up. I have
found that if I hit the jaws with a plastic faced hammer while I am
tightening my chuck I can get every bit of the runout out. Thinking
back, I've seen my friend and full time machinist do the same thing on
both three jaw and four jaw chucks. Is this a standard practice or am
I damaging my chuck?

Chuck is a new Chinese that came on my new Precision Matthews 13X40.
Spindle face runs true as does the chuck body itself as long as the
chuck is mounted in the same position every time. D1-4 mount. Never
had these problems on my old Sheldon 11 X42 but it was a well worn
machine of 1942 vintage