For two weeks i have had a cough every night and and i wake up with a sore throat and feel exhaustedno congestion. what should i take?

Acid reflux: You may have acid reflux. Don't eat late, avoid alcohol, if you smoke stop smoking and try Pepcid or zantac (ranitidine).

GERD: Best guess in short would be reflux. As long as you are not pregnant try some Prilosec otc and see if this helps over a two week period. If better, you'll have a good start and can continue discussions with your doctor.