Your work is the result of great research. You didn't ask about regimental references, but that's what you really want. Targeting a specific company normally yields no results. What you really need will probably be found with the regiment. Ken Jones has done great work assembling resources by regiment, battalion and battery for Alabama --
http://history-sites.com/~kjones/albiblio.html

Here are Ken's sources for the 49th Alabama Regiment, AKA 31st Alabama --
Sulzby, James Frederick. Johnson's Island reflections : a paper on the confederate prison at Johnson's Island, Ohio. (Birmingham : R.W. Beeson, 1988)
Taylor, Thomas J. "'An extraordinary perseverance'; the journal of Capt. Thomas J. Taylor, C.S.A.," ed. by Lillian Taylor Wall and Robert M. McBride, in Tennessee Historical Quarterly, XXXI (Winter, 1972), 328-359

if there's anything else, it's in private possession or in an archive as an unpublished manuscript.