Most often cough and cough in children is caused due to certain viral infections. Most often such infections are associated with allergic reactions which can be responsible for runny nose. It may also be associated with increase in temperature and muscle fatigue as in her case. The muscle fatigue is more likely to be the cause of her eye pain as well as her knees hurting. Giving paracetamol should provide relief for both fever and muscle pain. Giving some antiallergic like cetirizine syrup for a few days should help. Also give her steam inhalation. Water in the form of vapor reaches deep into the lungs and helps in diluting the cough and provides relief from dry cough. In case the symptoms last for more than 7 days or if the child grows lethargic or starts wheezing, you would have to take the child to a doctor without delay.