Have you seen the book by Cecelia Conway "African Banjo Echoes in Appalachia"? It covers that period, most specific to the Banjo. It is comprehensive in it's research but, I found, flawed in it's conclusions.

The best instruments for a Civil War reenactment are (proper period constructed types, of course) banjo, fiddle, guitar, fifes and flutes, accordian (lever-keyed, not keyboard), tambourine, triangle and bones, harmonica (kinda'). Leave the modern versions of these at home along with mandolins, bagpipes and dulcimers.