Lt. Col. was his brevet status...
Custer held the rank of Lt. Colonel in the post war Army. His brevet status was Major General. Custer was second in command of the 7th Cavalry. Regimental Commander at the time of the Little Big Horn was Col. Samuel D. Sturgis. Custer was field commander of the Regiment.
Sturgis replaced Col. Andrew Johnson Smith (also a brevet Maj. General) as Regiment commander in 1869.