Hi John,
I didn't interpret your comments as negative. Perhaps too many details about the backstory follow. You may have already been aware of some of these points, hopefully a bit or two will address the possible conflicts you raise.
1. More to do … Yes. You wrote, " I'm wondering if there are other wills that might give further information …"
We have many more wills to transcribe. Those doing the work assist each other and receive a helping hand from WikiTree experts. If you or others have an interest in this work, or would like to learn about processing English wills, please, please join us.
2. Why Hingham?
You wrote, "[Torrey] ... also only focused on information from Hingham and [did not look] at surrounding parishes that may give further clues."
Torrey was himself related to the Gilman family of Caston and Hingham (thus more closely associated with the Clarke family), but his work on the Lincoln-Gilman-Cooper-Clarke families extended beyond Hingham. Torrey knew Thomas Cooper was part of a migrating cluster[1] and believed he came from Hingham. In his notes about early settlers, Daniel Cushing wrote, "Thomas Cooper and his wife and two children and two servants and two other persons (viz:) John Tufts and Robert Skouling, came from Old Hingham, and thereabout, and settled in New Hingham."
Our WikiTree collaboration also extends beyond Hingham. Ann Browning routinely pulls identifiable parish records from surrounding towns. (See her comment.)
3. You wrote, "I find it a bit troubling that apart from [parish registers, Torrey] cites no other sources …"
Au contraire, Torrey referred to both "Daniel Cushing's valuable record" (also as "Cushing's record") and "Rev. Peter Hobart's diary." Both are reasonably contemporaneous records about the immigrants and were created by folks who had personal, first-hand knowledge of the families.
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Daniel Cushing (1619-1700),[2] from Hingham, immigrated with his father, Matthew Cushing (born Hardingham) and family. Daniel became Hingham's third town clerk (rather chatty in his record). See "Daniel Cushing's Record," The New England Historical and Genealogical Register, 15 (1861):25-27; digital images, Hathi Trust.
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Rev. Peter Hobart (1604-1679),[3] from Hingham, came to New England in 1635 and settled at Hingham the following year. Hobart ministered there, recording early baptisms, marriages and deaths. Torrey likely worked from a manuscript, but part of the journal was published as Andrew H. Ward, "First Settlers of Hingham," The New England Historical and Genealogical Register, 2 (1848):250-255 (marriages, etc. begin at 252; digital images, Hathi Trust. For the more complete, transcribed record, see C. Edward Egan, Jr., "The Hobart Journal," New England Historic Genealogical Register, 121(1967):3-25, 102-127, 191-216, 269-294; digital images by subscription, AmericanAncestors.
4. You wrote, "... I'm not sure on what basis he determined that Thomas Cooper 'the Grocer' was the immigrant, or that he was in the United States by 1639."
Aside from the record of Daniel Cushing, Torrey's reasoning applied onomastics to the England and Massachusetts families, as he devised them. Finding the names Nathaniel and Rebecca as English siblings of "the grocer" and as children of the immigrant, baptized Massachusetts.
There is a circular reference of sorts with the onomastics, as both records must be proven--and each provides support for the other.
Separate from Torrey's work, (a) English-born son, Thomas Cooper, baptized 1630, is about the right age to have had children born at Massachusetts in the mid-1650s. (b) Albeit light, there are some continuing onomastics--son Thomas has a child Rachel; daughter Rebecca has child Nathaniel; son Nathaniel has child Thomas.
