I think I can explain your 1860 Census problem for Thomas Daly and his wife Ann Dodd Daly...You have the right 1860 Census in Boston, Ward 9, p 169. There are three generations in the same household. Here is the breakdown of this family: The head is James Daly, a carpenter, (Born abt 1800 Ireland), next is his wife Anne Hickson Daly (born abt 1802 Ireland), then their son Thomas Daly, also a carpenter, (born 1828 Ireland), then James and Ann's son John Daly (born abt 1839 Ireland), then Thomas' wife Anne Dodd Daly (born 1829 Ireland), and then Thomas and Ann's three kids Sarah, Anne and James.
The 1870 Census for this family is in Boston, Ward 7, p 214. The Head is Thomas Dailey, a carpenter, (born 1830 Ireland), then his wife Ann Dodd Dailey (born 1831 Ireland), and then their kids Ann, James, Katie, Robert and Thomas. Ann Dodd Daly dies in September of 1870, just a few months after the Census is taken.
Another researcher said that the family is in Boston on the 1880 Census, but I have not seen this Census.
The marriage record for Thomas Daly and Ann Dodd Daly, as well as the christening of their oldest daughter Sarah Daly are in Killorglin, Kerry, Ireland and are available free at irishgenealogy.ie.
Sarah Maher, the wife of Thomas Daly, I assume to be an error in reporting from whomever was the informant for the death of Thomas H. Daley. This death certificate gives the name Sarah Maher as Thomas H. Daley's mother, but Thomas H. Daley lists his own parents as Thomas Daley and Ann Dodd on his marriage certificate.
Thomas Daly's second wife, Ellen Reilly, was married to a Healy before she married Thomas Daly, thus their marriage certificate is under Thomas Daly and Ellen Healy.