Custer started using the red over blue flag after Gettysburg. According to the literature that comes with Plate No 683 copyrighted in 1993 by the Company of Military Historians, Custer's first personal flag was used from Jul to Oct 1863. According to "A Compendium of the War of the Rebellion," Vol. 1, p. 462, the Cav Corps - Military Div of the Mississippi was not organized until Oct 1864, by which time Brig Gen Custer, USV, was on his 3rd flag.
Camps notes were scattered. The Siefert notes, at the time (1995) of the publication of Liddic's and Harbaugh's work were in the Western History Department of the Denver Public Library.