You also have the problem that you are working before formal registration of births, marriages and deaths, so will be relying on Parish Records, not all of which are on line.
The fact that his father died when he was so young could explain why he isn't with his parents in 1841 or 1851. His mother may also have died, or perhaps she remarried.
If the 1851 is correct and John is Sophia's nephew and Mary Sawyer is her mother, then it follows that Mary was John's grandmother. So his mother was Nancy Sawyer.