Rudi Geudens has written a modification of Richard Borg's Battlecry game for miniatures. You need a set of the original rules to play, though.
North Against South is a set of free wargames rules for civil war battles. It's based on the boardgame Battle Cry by Richard Borg.
Mike Callan offers this set of free wargames rules for American Civil War Ironclads. The set originally was published in Wargames Illustrated 14.
Peter Hunt of the Hong Kong Society of Wargamers has written a set of articles about Naval Warfare in the American Civil War. This is, I think, a sadly neglected period for wargamers. I have a couple of dozen ships in 1/1200 scale, and the games have always been well received.