Hello,
It has been a number of years since we corresponded re: Clearys. I think that your John Cleary was the brother of my Denis Cleary(b. abt. 1858 in Cork, IIRE). He had sons NAMED Thomas Augustine Cleary and James Cleary, plus others.
Thomas Augustine Cleary named one of his twin sons Daniel EUGENE and the other Thomas Frances Cleary.
The birth years, John 1855 and Denis 1858 and a third brother, Thomas F. 1859, would make sense. Hopefully you have discovered some info since 2000 as I have and we can share. Email me.