Dean -- Back in the Dark Ages (when I was an apprentice) we used a system whereby (1) we made a plate with a (standing "proud") X and Y (square) index edges to which were located three very precise "disks" with an accurately bored centerhole to position the center of the to be bored hole. The location of said "disks" were such that the bored centerhole was at the precise location when the (three) "disks" were mounted (over the "working material") to the X and Y index edges and tangent to each other. Thus, we could dial in the centerhole and be "on" within the tolerance of the indicator (usually .00005 inch). The bored centerhole was large enough that we could "spot," drill, and ream/bore through it without disturbing the set-up.
I was burned out by an arsonist/thief in December of 1974, but I used to have a "roll away" chest that was filled with several hundred pounds of such "disks." Back then, having such a "collection" was one of the hallmarks of a machinist who could work to great precision. It is a labor and time intensive approach, but it was the way truly precise hole locations were laid out in the days before accurate way indicators were available. ???