The letter that my grandma's cousins wife wrote stated that Thomas was a shoemaker and that he ran a store in Vernon, Ontario but I am not sure if that is true. John was a farmer so I always thought that his dad would have farmed as well but there is no source for that. But maybe Thomas wasn't qualified to be on the tithe books.
That's an amazing point about religion and spouses. For years I had Thomas who married Mary Williamson as the mother of John, since it fit quite nicely with the parish records for BDJ only starting in 1826. And if Mary died, and Thomas married Harriet ----, she was born in England according to the 1861 census, so she would have been Anglican and maybe that's why Thomas was supposedly buried in an Anglican Cemetery - that always struck me as strange since John was a Methodist but John's wife Eliza's family, the Little's, were Methodists as well so maybe that's where that came from.
Thank you for your input. A fresh perspective can really help!