A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of servo sectors defining a plurality of servo tracks. The servo tracks form a plurality of servo zones. A disk locked clock is synchronized relative to a servo data rate of the servo zone the head is over. A first reader/writer gap is measured in cycles of the disk locked clock at a first servo track in the first servo zone. A second reader/writer gap is measured in cycles of the disk locked clock at a second servo track in the second servo zone. The first and second reader/writer gaps are normalized to generate a normalized first and second reader/writer gaps. A third reader/writer gap is estimated in cycles of the disk locked clock at a third servo track in the second servo zone based on the normalized first and second reader/writer gaps.