Neck Pains Due To Hard Cough, Ammonia Smell In Poo. Took Neurofen. Right Medication?

Have been coughing so much and hard that now have a very painful neck up top where head joins, taking neurofen and this takes the pain away, but pain still there when pill wears off. did not take pain killers for first few days and suffered sleeping really painful lying down. Had stiff necks before but this is something else. How long till better do you think. Cough was green and always worse at night but is on the way out now, also poo yesterday very amonia smell, not as bad today, have been having a lot more acid than usual as loads of squeezed lemons and fresh ginger so that and virus/infection may have messed up my good bacteria etc for digestion.
Cheers