To properly do a bolt stretch study, you need to have both ends of the bolt ground flat and parallel and center drilled... Then use a ball micrometer to measure the bolt from center to center on the ground ends... That way you are sure that you are measuring the axis and are not thrown off by not being on the center of the bolt, any mismatch/off center will affect your readings...
And yes, you need to use micrometers, not calipers... One of my coworkers did not follow my advice on that and had to redo his study as the calipers are not sensitive enough to give an accurate reading for bolt stretch... Calipers can only measure to the nearest thousandth, micrometers can measure accurately to the nearest ten thousandth... You need that accuracy to get proper readings...