Richard,
Since your primary datum is surface D, you should measure the 2 bores as cylinders, intersect each with the plane, and use the points (or diameters) on the surface to make your alignment.
Duane Wade
CMM/Gage Technician
TeleFlex Automotive - Pedals Division
301 W Ohio St.
Kendallville, In 46755
219-349-1985
dwade@tfxauto.com