There are many Mississippi Confederate records here that not transcribed yet. Many you probably seen, others are new to me. You have to really search each section because they did not organize these well. To start go to...

http://www.mdah.ms.gov/arrec/digital_archives/governmentrecords/

You can select

* Auditor, Mississippi Office of State
* Confederate Records
* Federal Records > County Rosters of Military Veterans (The series is made up of copies of rosters culled from county records, newspaper articles, and other sources that list Mississippi veterans (and widows and servants) of the Civil War, the Mexican War, the Spanish-American War, and the War of 1812. These records were compiled as part of the Mississippi Historical Records Survey by employees of the U.S. Works Progress Administration between 1936 and 1939.)

and many more. Have fun!