Do you know about the 1869 book at the Washington County Free Library - Full title (!): Descriptive list of the burial places of the remains of Confederate Soldiers, who fell in the battles of Antietam, South Mountain, Monocacy, and other points in Washington and Frederick counties, in the state of Maryland"? It is viewable online from WHIBR: http://www.whilbr.org/confederateSoldiers/index.aspx

A high proportion of these were "unknowns", and I expect many/most were re-buried at the Confederate Cemetery in Hagerstown after the War, but this might help with part of your quest ...

Regards,

Brian Downey
Antietam on the Web ( http://aotw.org )