Okay, so this is pretty embarrassing..
I cannot remember what I did. Ironically enough, I actually did a playthrough of the game for YouTube. So I decided to just re-watch that and.. I cannot believe I am saying this, I told myself in the video, "I am just doing a general play through of the game, if you want to know the actual details, go find a walkthrough."
Jesus Christ I think I just trolled myself. I need to re-play the game and do a better job. I don't know what I was thinking!