Help with programming/report

Help with programming/report

I am hoping someone can give me some idea on the correct way to program/report this part.  Currently I am measuring datum A as a plane and leveling, measuring a circle around datum B for my origin, and then measuring datum B as a cylinder and aligning the model from that. My CAD model is in sync. When reporting the TP of the .500 diameter thru bore, I am getting .003". I have gone as far as setting the part up in a 4 jaw on the lathe and measuring with indicators, showing maybe .0005" runout, which is not giving me much confidence in the CMM results that I am getting. I understand that I can't compare apples to apples, but my indicator readings are suggesting that I am doing something wrong either in my alignment or report setup on the CMM.