Oral HPV caused from sexual relations is highly rare. You mentioned you went to the doctor, what did he say these bumps were?
I am no doctor but I can tell you that the only way to find out how to cure these bumps is to go through a trial & error process. If they are that annoying, inform your primary care provider (regular doctor) and go from there. He/she should give you options on how to remove the bothersome bumps sooner than later. I'd say that, if this an HPV-related situation, you should maintain a healthy diet. HPV is funny that way; your diet and all-around health/hygiene affects what goes on. If you smoke, you should stop (at least for a while.) If you don't, eat better and keep checking in with your doctor until you find a routine that works best for the problem you have.
Don't sweat it too much. Live your life and do what is right to rid yourself of these annoying bumps. You'll be fine.