Pete Pellegrino has written a set of free miniature wargames rules called Damn The Torpedos. In the game, you customize your ironclad, and then take it out to fight in the Cvil War battle of Mobile Bay.
Heart of Oak, Skin of Iron is a set of free wargame rules for naval combat in the years 1852 – 1870.
A Hotter Fire is a set of free wargames rules for naval comabt between civil war ironclads.
From the Naval Wargames Association comes Ironclad, a set of free wargames rules for ACW ironclads.