All teeth are connected and all organs are connected. I have had this experience before, where you think one tooth is hurting you, but it turns out to be another. so i usually wait a couple of weeks and the pain does eventually target itself in the right tooth. But in your case, you have done the right thing to take out a root canal tooth, because they should not be in your mouth anyway. Is the one that's hurting you now, is that a root canal tooth as well?