I spoke with Frank Fox, and he pointed out the captains list in "Pepys"

I spoke with Frank Fox over the weekend, and he pointed out the list of captains who served during the period of 1660 to 1688 in the Navy Records Society publication: A DESCRIPTIVE CATALOGUE OF THE NAVAL MANUSCRIPTS IN THE PEPYSIAN LIBRARY AT MAGDALENE COLLEGE, CAMBRIDGE. Volume I: General Introduction; Register of Ships; Register of Sea Officers. I have already used it once, since then, in writing about an English captain (Edmund Cubitt, I believe).