Frank, thanks for replying!
Brain fart on the cousin definition. I was looking at the shared cM chart, on DNA Painter, while too tired! :) Yes, you are correct, John and Mary and 1C1R. John's grandfather is Mary's great-grandfather.
I reviewed all the hypotheses and also felt like #11 was the most likely, probable scenario. Since my father and Les do share DNA, then that excludes my grandmother being a full child of one of Thomas' descendants or her being a half-sibling of John or Mary. Other hypotheses that would make my father the child of someone born in the 1880s also don't make sense. So that eliminated a lot of the choices, besides that probability score being so low. I'm glad that you came to the same conclusion.
I definitely have been trying to dream up scenarios! LOL! :) It's not that I don't want to believe it, but 1) like any science, it's good to get theories reviewed 2) I was diagnosed lupus a few years ago and the disease and all the meds I'm on have affected my cognitive function and I really doubt myself a lot these days 3) I also really don't want to tell my father because these are his favorite grandparents and he'll be really disappointed. So I really wanted to make sure what I was thinking was correct.
I had uncovered, a few years ago, that Harold, my father's mother's father had a different father than we all knew about. His surname was Pitman, which was my grandmother's surname. But it turns out he was born to William Kinzey, who died when Harold was very young and Harold's mother remarried, changing Harold's surname to her second husband's name. This was news to my father and his cousins! William Kinzey had many children with his first wife. A descendant of William's first wife, who would be my father's and Les' half 2C2R, found me online and we shared information. He did an Ancestry DNA test and uploaded to GEDMatch and my father does not match him, but Les does, at 20.6 cM on one segment. That relationship, half 2C2R, could result in zero shared DNA. So this doesn't help too much. Most of Les' matches don't have tree, don't communicate and don't match on X, so I've struggled to determine any other Kinzey matches. Should I focus more time on finding Les' Kinzey matches to determine if any match my father?
My father does have a bunch of matches to Thomas' relatives. There is one match on MyHeritage of 170 cM, from Spain, that triangulates with Mary, and after bringing Spain into DNAPainter, they also have a large segment overlap with John. There are some other matches that triangulate with John or Mary as well, I have ten besides John and Mary in a match group on DNA Painter. Another one, that is ICW Mary, is a 42.6 cM match from Australia that also overlaps with John in DNA Painter. Australia carries that same surname as Thomas and Australia's ancestor is from the same town in Ireland that Thomas is from, but emigrated to Australia, instead of America. I haven't found their shared ancestor yet though. I'm going to have to learn how to research in Ireland! Of all the matches of my father's that I can confirm match John and/or Mary, none of them overlap with Les. Do these additional matches change your conclusion at all?
My father tested at 23 & Me, which is where he matches John. I uploaded my father's test results to MyHeritage, which is where he matches Mary, Spain and Australia. I also uploaded Les' test results from FTDNA to MyHeritage and he does not match Mary, Spain or Australia, confirming what I see in DNA Painter. John's daughter is on GEDMatch, but John is not. John's daughter is not in Les' match list on GEDMatch. Does any of this make a difference?
As far as matching Thomas' wife. I am not distinguishing between Thomas' and his wife with their descendants. I know Australia is related to Thomas. I do not yet know of the relationship between Spain and Thomas vs. Thomas' wife. I'll keep this in mind, for sure. At this point, do you think it's important to differentiate between Thomas' and his wife?