Both Auburn University and University of Alabama have excellent archival resources. For that matter a researcher can spend time profitably at a number of Alabama college libraries. Samford University has a wonderful collection that I literally dream about. West Alabama (Livingston) has a published collection on the web that's quite tempting. Wallace State (Hanceville) has large collection of microfilm from the National Archives and other state archives.

Can't think of any archival resource in Alabama that treats Confederate material differently due to what some people might think.

Tim, call or visit the Department of Archives and History in Montgomery and explain what you have. Their people -- just like any other professional archivists -- can offer good advice. If you haven't been to Confederate Memorial Park just down the road, ask Bill Rambo about the journal (and pass along my regards). People donate documents to CMP, so Bill can speak with you on this subject.
http://www.museumsusa.org/museums/info/1154229

Unfortunately I'm now living 1,800 miles away in Maricopa County AZ. Temperatures have been slightly lower than in Alabama, but that should change shortly. History has a different focus here. After reviewing topics to be presented at the Arizona State Historical Society annual meeting in Phoenix this month, my wife suggested that we might as well be from Mars.