hello David,
I know this is some years since you wrote your query and may now have the information you were looking for! But if not I can tell you some more about Thomas and Rachel as well as Thomas' parents. We are , I think, distantly related but it is confusing because there were 3 John O'neils born around the same time.
Any way as you say a John O'neil was born in Prescot to Thos O'neil and Rachel formerly smith in 1812 .He has siblings Susanna, James , Thomas and Elizabeth. He was the youngest. His father Thomas was born in Prescot in 1777 - father Michael(died1788) and mother Ann. He was baptised in the Portico Catholic church and this is where many of those early Prescot O'Neil records are . (sorry I don't have these records, but was given some names and dates by another researcher). I didn't ever know what hppened to this John.
Michael O'neill and Ann had a son John born in 1787 in Prescot . He married an Elizabeth Houghton and they had a son John in 1811. this second John seems to be the one who marries Margaret Hughes in 1832. What is slightly puzzling about this John is that when he married Margaret he gives his occupation as" blacksmith" and this is why for a long time I thought he was part of my O'neill family.
My family is William O'Neil, a blacksmith born 1793 probably in Prescot ,possibly the son of a Patrick who I think is Michael O'neill's brother .William has the third John - born 1814 - who again disappears without trace (no death record) William also has my 2x gt grandfather Edward O'Neil born 1821 in Prescot (William O'n and Charlotte nee Lyon) .
Who might be Michael & Patrick's parents? well, there is a slightly mysterious rev. Felix O'neil who has a son John in 1740 in nearby Rainford and later baptised when Felix is minister in Bolton le Sands. I've not found a baptismal record for Michael but he does have a son Felix.
I hope this is some help to you . Are you certain your ancestor was the 1812 John? And if you or any one else reading this can fill in any of the many gaps about this family I would really appreciate it.
kind regards,
Alison
Taupo, NZ