Correct alignment for runout dimensioning

My searching and reading has informed me that: 1) I know what I need to learn 2) learning it is going to take longer than I have right now.

Please forgive my horrid sketch. Running PDMIS CAD 2016.

I have a ball with a bore all the way through. Perpendicular to the bore and 180 degrees from each other are 2 cylinders. Datum A Cylinder is in the bottom of a slot (so it has a flat surface that can be measured as a plane and used to level). Cylinder PITA is called out: runout 0.004 to Cylinder A.

I believe that in order to dimension this correctly, I need to:
1) measure the plane and Cylinder A
2) level to the plane
3) translate origins to the center of Cylinder A and the plane.
4) I'm unsure about what to rotate to in order to complete the alignment correctly.

After this, I measure Cylinder PITA and click on the report icon for the runout dimension. I know it makes a difference which cylinder I click on first and second in this dialog window, but cannot find clear instructions telling me which one should be first or second.

(I REALLY wish I could get a Matrix-style download of the knowledge I need right now... I just can't learn it fast enough to satisfy myself!!! Grrrrr!!!)