What could cause a sore throat, headache, earache? I saw a doctor a week ago and he said my sinuses may clogged up and should have been better by now

Upper respiratory in. Common cold or upper respiratory infections are caused by viruses that don't respond to antibiotic. Most cough illnesses last 18d on average and will take same amount of time to recover whether you take antibiotics or not. Symptoms of URI are exactly as you've noted above. Supportive care in form of over-the-counter meds can help alleviate symptoms but won't speed up process. Stay hydrated.