So I'm currently level 42 and was shocked that the story line just abruptly stopped when I was around 35, after killing the guy who goes bad out of "the five, anyway.... I was wondering what I did wrong and what I can do to fix it
You'll have to finish the Coldharbor zone in order to pick up the very end of the Main Quest. You should get a quest to meet the Alliance leaders at Stirk that starts the Coldharbor zone. Finish that zone and the Prophet will start giving you the final Main Quests.