Phase locked loop is a term borrowed from electronics. It refers to the
method of tracking a signal that might be varying by comparing the
difference between the timing of the signals peaks and valleys and that
of the signal that is being matched to it. This is what is referred to
as phase difference. This difference is used to adjust the second
signal to match the first.

Wayne uses a similar technique to make sure that the information he is
extracting from the piano rolls matches the original master. The master
was punched at a fixed rate and this  frequency can be determined and
compared to the note data coming from the roll as it is scanned. The
difference can be used to adjust the scanning procedure.