ok found the bad code in the sidebar. It was related to "My recent posts" block. I have re-enabled the sidebar but disabled that one block for now. Things seem to be running ok. I am now in contact with vBulletin, turning over all of our config files so they can help us optimize the server. The next couple days I'll be focusing on that. To give you an idea of how the large threads+bad code in the sidebar issue affected us:
The above chart is for the last 3 days. You can visually see the massive problem arise and fade away once it was resolved. I certainly learned a lot during this drama. I had never really needed to go into the database console to troubleshoot. I have a much better feel now for drilling down to issues from the server application level.