I've since found that William A was married to Mary Adams in 1867, after John T was born, so he is most likely out of the running. I've found civil war records that Isaac served in Company F of the 47th Tennessee Infantry (mustered in Humboldt) and seems to have been reorganized into the 6th Tennesse Infantry. Both units served at the battle of Chickamauga. I've found some people who state that he died there in 1863. This would eliminate him also.
This leaves James Dungan and the only remaining candidate (if the status in the census of Cousin is first cousin), but I can't find any information on James Dungan. If anyone has information in James Dungan born before 1846 and died before 1923 (sister Mary Jane's obit only lists brother T G H Dungan as survivor), I would greatly appreciate it.