I just saw your inquiry today.I am descended from what I believe is the same branch of the Hughes family as you have mentioned.
I am in possession of a letter dated 1903 from a John Hughes of Blackstock Ontario, which provides a good amount of detail.I will scan it and e-mail it to you, if you desire.
To summarize the letter:
Originally, a Hughes from Wales came over with Oliver Cromwell's army in about 1649 and settled in Clones, County Monaghan.He married an Irish girl and had several children.One of them was named Phillip.Eventually two of Phillip's sons (William and John) moved to the Belfast area and two other sons (Peter and Phillip) moved to County Tyrone - the letter mentions Cookstown, Dungomon (Dungannon), and Omagh for the family of the younger Phillip, as well as Fintona for John's family who were descended from James, who had joined the British Army in 1803 and served until 1821 in Calcutta, India.
There may be one or more generations missing in the names listed above or in the letter.
The James you mentioned was descended from the younger Phillip.That James had brothers named Peter and Phillip.James had three sons - James (who I descend from), Daniel, and Peter.The son James settled in Jackson TN.The chart accompanying the letter lists names for children of Peter and my James, but not for Daniel.It says that Daniel died in Cincinnati.
Finally, although the original Irish Hughes ancestor (from Wales) would have been a Protestant, my James Hughes was Catholic.He was a tailor and eventually became postmaster of Jackson TN.The first Catholic services in Jackson were held in his home until a church was built.He was married in Jackson TN on January 1, 1833, so he would have arrived in the US before then.
I would be happy to share what information I have with you.
I would also be interested in finding out what you have discovered, especially about Daniel's parents James and Elizabeth.