If it were me, the next three things i would try (which you have possibly already tried) are 1) to contact the local history people and see if you can acquire any memories booklets or things like that, in case your wife's family members are mentioned.
2) try to follow the land ownership of both John and his kids and James and his kids, especially what happened when James passed away
3) try to figure out how John and Rebecca met in about 1846-47.
James might have been enumerated in 1841, if the information given to the 1851 enumerator is accurate - that the younger two girls were born in Canada...there might be some clue there, if that record can be found. Also, the woman living with him in 1851 might actually be his sister, since she is said to be a spinster....