I just got over the flu, but have a lingering cough thats pretty harsh. My lower abdomen now hurts rite above my waist line appendix or muscle?

Common problem. It is common after a viral infection resolves, that a cough may linger. It generally resolves within 8 weeks and is called a post-viral cough (duh). To cough, you use abdominal muscles but with excessive coughing these become sore. If a fever returns, fatigue continues, productive cough or breathing difficulties develop, see a doctor. A mild pneumonia/bronchitis can follow viral infections.