I got the two Joseph F. Thompsons mixed up.
Corrections noted: Pvt. Joseph F.Thompson (1861-1863) of Capt.Johnson's Spy Company was from Snow Hill and not Major Joseph F.Thompson of Col. Stand Watie's Cherokee Volunteer Regiment. I suspect that Major Joseph F. Thompson was one of James G. Thompsons sons, especially since his mother was quarter-Cherokee and James G. Thompson was raised with the Cherokees. Judge Thompson had 18 children and ten survived to be adults.