Re: John Waller b. 1625
I did some more research in the Merchant Taylor School of London Register and I found records of some William Johnsons, but none of the right date for the one who came to Northampton Co. VA in 1654.However, one record was old enough to have been his father. But there were also records of several Wallers, the most interesting of which was for the entry on p. 138 dated 11 Mar 1634-35, of a Thomas Waller who was born 11 Sep 1621 and a John Waller, born 6 Oct 1622, who may very well be the headright of William Johnson in 1654.
Checking the LDS IGI Parish records for London, I found a John Waller, bapt. 27 Oct 1622, son of a John and Phillis Waller at the Church of St. Botolph without Aldgate, London.
It could be that he named his son William after William Johnson.
I know that traditionally, your family always thought that your John was the John Waller, age 17, who came to VA on the "Transport" which left Gravesend on 4 July 1635, but there is a lot of circumstancial evidence that this one was the youngest son of Robert and Ann Waller of Beaconsfield, Buckinghamshire, and may be the same John Waller who died in Ware Parish Gloucester Co. VA in about 1688.