The one in particular that I am looking for has Alley Oop as a sailor on the CSS Albemarle, the ram/ironclad that was blown up by a spar torpedo during the War Between the States. That was one of my favorite Alley Oop comic strips by far!!!

Also one of my favorites! The story you're looking for was run in the latter half of 1987 and was, in a strange coincidence of timing, reprinted for the very first time just last month! If you look for the book "Alley Oop Under the Sea", that's where you'll find that "Sink the Albemarle" story.