I'm relatively new to this (six months), so I maybe looking at things you've already explored. I'd be interested if you could add anything in the following areas:
Jeanne Kersh has mentioned that John and Catherine would have had another sister by these parents. Her research shows there was a Nancy born while the family lived in War Eagle Township. She married a Hewitt and moved to TX. Her headstone shows a date of birth of 1835. Have you located the 1840 census? Do we maybe have an unaccounted for 5 year old girl?
To keep my questions separate, I'll post two more follow-ups.