Why are there no records of John’s and Nathaniel’s arrival in Portsmouth, NH? Usually, there are ship passenger records. Not for Puritans in England during the 1640’s, 1650’s and 1660’s. King James did not want his church “purified” by these malcontents many of whom were successful businessmen. The wealthier you were, the better for the King’s taxation so successful Puritans could not receive permission to leave from him. Poorer Puritans could only have permission to leave if they had a “certificate of conformity” (a loyalty certificate) from their minister. Many arrivals to Puritan New England were hoping to worship in peace according to their own ideas and so came without permission. Only those legally leaving England were recorded.
[See: Samuel R. Gardiner, History of England, From the Accession of King James to the Outbreak of the Civil War, 16.3-1642, vol. 8, p. 167 & 169. Also: Daniel Wait Howe, The Puritan Republic of Massachusetts Bay in New England, p. 9.]