John,
The flag of the 46th Miss. is in the Illinois State Military Museum, Springfield, Illinois. Fragments of the 35th Miss. flag are located in the Minnisota Historical Society. The 40th Miss. flag is in the Iowa State Archives in Des Moines.
http://www.mississippiscv.org/surviving_ms_conf_flags.htm
This address might help you find the Mississippi flags you're looking for.