Yes actually I found much more information.I purchased those two records (what a RIP OFF that site is!!!) and both we are petty sure are not the right Thomas.They were located in Clonmel and other areas and I think there was evidence they may well still have been in Ireland after my Thomas was in Canada. We think he was in Ballybricken.
Or oral history passed down by our grandfather was always that we had Catholic priests in the family and that Thomas was the last male to carry the name, and he left from Ireland to Canada.Thomas was the youngest and the other brothers didn't have males that survived or they were priests.Thomas actually was involved in supporting and building two catholic churches I could find.One in Ottawa area and one in the St Thomas area.
In regards to the Waterford conneciton - It seems that we are related to Peter James Kenney, who was a Jesuit priest who founded Clongowes Wood College.Thomas actually swung by Pennsylvania the same time Peter came to PA.I can't directly link him to Peter yet but so far I've looked up Peter's brothers and one of his brothers was from Waterford and befriended Edmund Ignatious Rice around the same time Thomas was born in Waterford.There were only a few Kenney's in the Waterford area in that time period.Peter's father was known to be from Waterford and had a business there would travel to Dublin and back.He also remarried we think.
There is a 500 page book on Peter James Kenney that gave me a few clues to follow.Since the oral history of our family and some of these things matched up it is almost certain that we were related to the Waterford Kenney's.We know that it is spelled EY, that most of the records I've found were misspellings by the transcriber.People generally don't add an E they omit it.(I know this from experience)
I did a DNA test so I should have results soon, maybe I can hook up with some long lost relatives :)