Abstract: A disk drive is disclosed comprising a head actuated radially over a disk, wherein the head comprises a read element separated from a write element by a reader/writer gap. A disk-locked clock synchronized to a rotation of the disk comprises a plurality of clock cycles, and the reader/writer gap spans a first number of the clock cycles comprising a first integer of the clock cycles plus a fraction of one of the clock cycles. A reference clock cycle of the disk-locked clock is determined, and a write operation is delayed relative to the reference clock cycle by a write delay comprising a second number of clock cycles comprising a second integer of the clock cycles plus the fraction of one of the clock cycles. A sync mark is written on the disk after the write delay, and the sync mark is read to estimate the first number of clock cycles.