Your John, born 1812 is definitely brother to my (and ParticiaMc's husband's) Thomas 1818 gggf. The 1861 Canadian Census is especially illustrative in showing the parallel families of the four brothers, James, John, Daniel and Thomas. Original-John's Thomas, your g grandfather, does show having been born to John and Margaret in 1855. I've been able to cross-reference some of the information with an old family bible dating from the days of Original-Thomas. In it is recorded that "John (spelled) Danohoe died Oct 26, 1866 age 54 years" Also is recorded the death of their mother, Elisabeth (sic) (Cain) "died Aug 28 age 90 1866".
The duplication of given names, even within the one generation down from the original four brothers... Not to mention the unbelievable variations of surname spelling (or census takers' penmanship)is extremely confounding.