Hi Bob! Thanks so much for the comments. No, unfortunately, I do not know the name of John Fernald 3rd's wife or his children. Sister Miriam Fernald was born 1765-1770. When her father John Fernald died in 1794, he divided his estate between two children, my Miriam (Fernald) Lewis and her brother referred to as John 3rd, who I presume was born somewhere around the time Miriam...1760-1775. By the 1790 census Miriam Fernald and Paul Lewis were enumerated as a young married couple alone in Kittery and not near either John Fernald.
I see in 1790 John FURNAL 3rd with 1 male 16 or over, 2 males under 16 and 3 females. Also a John FURNALD with 1 male over 16, 4 males under 16 and 5 females. Then there is a Jno with 3 males over 16 and 3 females, but that would be Jonathan. There is also a Joel Furnald. You said there were three Johns, but I might have missed one. I must go over to Alfred to get a copy of the actual estate division to see if John lived in the Upper or Second Parish that became Eliot or if he lived in what stayed Kittery. There may also be something in deeds there.
Have you done a lot of Fernald research in Kittery/Eliot? I have looked at Stackpole's Old Kittery Families, Kittery vitals, census records, Eliot town history, 1837 Eliot school census where all members of household are listed and Maine probate. Were it not for the old bible and its records, I would not have had any idea about Miriam and Paul Lewis being mine. I had looked for the parents of Miriam Lewis (daughter of Miriam Fernald) for a long time...there were sooo many Lewis families...and then found the bible on ebay!
Let me know what you think, and also tell me if I can do anything in Kittery or Eliot for you. I have ancestry in both places and have done a lot of research concerning both towns.