You make an interesting point about there possibly being two Nathaniels. I don't know of Hiram ever living in Livingston County, New York. Where in Wisconsin was Polly? Hiram and his family were in Winnebago County, which abuts Wisconsin. Let me know how your research progresses and maybe I can help. I would love to solve the mystery of Nathaniel. I found Hiram's parents on his marriage license to his second wife (they were married in Wisconsin). Hiram's parents were listed as Jno (John or Jonathon) and Lucretia Putney. But I was unable to take it further than that despite several hours of research in Salt Lake last spring. There are numerous Putney families and I suspect most of them are related, but I don't know how. I have sporadically researched Nathaniel,thinking he might hold the clue to Hiram's ancestry, but always hit a dead end with him.
I have some Putney research done by others that you might be interested in....e-mail me your address privately and I'll send it to you. Might be a clue there that I haven't seen, but you would.