Correction to my own question. Although it appears that John Farley born ca 1647 is indeed a grandson of Thomas and Jane, Archer is not necessarily his father. Archer may not even be the son of Thomas and Jane's name.
He may belong to George, Thomas' other son.Further research is required. All I can say for certain is that Jane would have been too old to have born John born ca 1647/50. The 12 generations of Farley's can't be correct in assigning John as one of the sons of Thomas and Jane.