Hi Brenda, nice to meet you. Yes I agree the link between Daniel and John or Thomas is certainly not proven. Can't go into detail from a cellphone so maybe if you could take a look at some of my documents on John's page and we can talk more. I'm traveling until Wednesday. I have been tracing all of John's children to see their migrations and connections.
You might take a look at my research in William's line. There are some interesting finds there. As I recall Capt Asa Bly of New Bedford is linked to him through Asa Bly of Harmony New York.
According to some of the earliest genealogists, John was connected with Richard Bishop early in Boston. He may have had a first wife. Thomas Bligh arrived the same time as John. He stayed in Boston but was in evidence in Salem with the militia. Daniel appears first near Salem in the only records I have found. No solid proof, only soft evidence yet between those generations. I will check your tree out as soon as I get home.
Judy