If I get this right, you are trying to pivot the camera to get the left and right points on the back of the skull equidistant? That can only work if the camera is located along the right axis (imagine a triangle, whose base is determined by the two L/R points, the axis is at the midpoint of that line and at 90º). If the camera is not along that axis, then you can only rotate it to get the base line in focus if you first get the camera parallel to the L/R point line, and at the same time, use just the right amount of shift, to get back to the center line...
Again, this is assuming everything in the camera is parallel too, including the front lens plane. Sometimes that can be off. I had a heck of a time with a 35mm lens wide open, never could get sides both in focus. Didn't matter stopped down, tho.
Hope this helps.