The Pink Palace Museum has Civil War artifacts on display all the time including two CS flags. One, a large First National, was taken from the Memphis Post Office when the Federals captured the city on June 10, 1862. The second flag, the Mobile Depot battle flag of the 22nd Tennessee Cavalry (Barteau's), was issued in July 1864 and captured in Memphis in August when Forrest attacked the city. I think they have one more flag but I do not recall any Mississippi connection for it.
Greg Biggs