TrailMaker004,
I would say your dillemma is very common issue amongst CMM operators - you automatically look for fixed X-Y origin for measurements of studs position, which is reasonable practice in general, but does not always have to be a case. On the contrary, in this particular situation - when spacing within the pattern and its perpendicularity to A is checked - if you use one of the holes as a starting point for the other, you may end up with rejecting good part or, even worse, accepting bad product.
Like I mentioned earlier, the tolerance zone for the pattern of dia. 122 and dia. 121 studs is two cylinders, one of .001 diameter, second of .002 diameter, which centers are spaced basic .390 apart and perfectly perpendicular to datum plane A. These two cylinders can float together freely within tolerance zone defined by upper segment of composite positional FCF. This means there is no "global" origin that these cylinders are located from, as well as none of them is a starting point for the other.
Your next question also stems from very common misconception amongst CMM users. There is no single point (or level) along stud axis at which the measurement should be taken. The FCF says that whole axes of studs must be within cylindrical tolerance zones. Unless both axes are perfectly perpendicular to datum plane A, which is very unlikely, there is no chance to describe the axes as single points with x,y coordinates only. One must verify whether lines fall within cylinders of certain size, not points. This in consequence requires probing each stud at least at two levels in order to find two center points that could be used to derive a line approximately reflecting the axis.
If I were to measure the studs and verify this particular composite callout, I would try find the axes as-described above, and then see if they fell within tolerance zone as-described in second paragraph. Since two cylinders of the tolerance zone were free to rotate and translate, it would be possible and probably necessary to use a best-fit routine to adjust actual axes with their tolerance zones. Right after I found a configuration meeting the requirement, I would check whether it satisfied requirement expressed in upper segment of composite FCF as well. If it did not, I would iterate until satisfactory configuration was found or until I was 100% sure that such configuration did not exist.