Hello, Peter The Cains were Church of Ireland well before Thomas,from the early 18th C when they were still O'Cahans. John Cain, father of Thomas, appears in several records ca. 1803-1847.
Captain James Cain (1803-1848) of Melbourne, your native city, may be of interest to you as he was merchant with interests at Port Fairy ca.1840s and also a ship-owner. That may explain how Thomas's sons, John (1823-1892), William (1827-1888) & Thomas (1829=1877) voyaged to Port Fairy in 1848 without leaving a shipping record. Captain James Cain lived in London in the 1820s-30s like Thgomas & may be connected to him.