Just stumbled on to a good resource for Militia operations during the period following the fall of Little Rock until the end of the War.

Reynolds, John H., "Official Orders of Governor Harris Flanagin", by Publications of the Arkansas Historical Association, Volume 2, Arkansas Historical Association, Fayetteville, Arkansas, 1908, Page 362,

This has the Governor's Orders issued from July 1863 through November 1864 and has a lot of detail concerning the organization of various State Troop Organizations.