Is there any specific reason that the skirmish ruleset MUST be civil war themed? Weapon wise it's hardly a stand out conflict - muskets, pistols, swords, pikes etc.
Most man on man skirmish rule systems will do the job. . Really you could just pick your favourite pre-modern skirmish system and use that.
Test of honour would probably work really well of you just renamed the units. I can see mordheim working quite well if you simply stick to empire Vs empire warbands.
Blood and plunder could be a pricey way to do it if you just ignore the boats.