So I found Rigger Greene in the whirlpool area, freed the gremlin, talked to the pirate and went on my way. I talked to him 3-4 times before leaving, because it never updated my quest. I figured it would just complete it when I went back to talk to Horace though. So when I got back to Mean St I went & talked to Horace, he just gave me more new missions. He never said anything about the pirate, and the quest is still sitting in my queu. What did I do wrong, and is it possible to fix?
How many times did you talk to Horace? One issue with the NPCs in this game is that when they have multiple quests available they only clear one at a time, and rarely in the proper order (new ones take priority over clearing old one,s for example). Try talking to him several times until he starts repeating himself. If you freed the pirate then the mission should clear on like the third dialog or so. Also, a way to double check is to go to Ostown. If you did the quest right then the pirate should be next to his cousin and his house. You don't need to do this to complete the quest though.