Closest Points without Duplicates

Hi,

    In my file (which is attached), I am trying to get the length of lines and the radius of spheres based on the distance from the center of a hole.  The problem is that I am getting duplicates and the distance from point to point is getting confused with the duplicates.  For example, a point that is among the cloud for both holes is getting the distance of the further point rather than the closest point.  Any help would be great, I've run out of options personally and I've searched online but haven't seen any help.  Thanks.