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I descend from Thomas Bagnall and Ann __?__ who married about 1779. Their children were baptized in or about Manchester, Lancashire, between 1780-1803. Some were baptized at Manchester Cahtedral. Three of the children were Samuel Bagnall (my ancestor), baptized 1792, Thomas Bagnall, born about 1786 (I have his death certificate in 1850) and John Bagnall, baptized in 1795.
I am thinking that the Thomas Bagnall, born about 1786 might be the father of your Samuel Bagnall who married Elizabeth Jones on September 3, 1849 at Manchester Cathedral. This Thomas Bagnall married Mary Caldwell. I have a (partial?) list of the children of this Thomas Bagnall taken from the baptism records in the IGI and there is no Samuel Bagnall. Nevertheless, Samuel might be another child. This Thomas Bagnall who married Mary Caldwell was not listed in the IGI baptism records either.
If this Thomas Bagnall and Mary Caldwell had a son named Samuel then all the facts you mention would fit the marriage record of your Samuel Bagnall in 1849 at Manchester Cathedral. The John Bagnall, witness would be Samuel's uncle, brother to Thomas Bagnall.