Had URI for about 2 weeks. Sore throat throughout. No fever, and congestion gone for a few days, but still sore throat off and on. Allergies?

You are absolutely. Right. A lot of times you will still have mucus draining in the back of your throat causing you to cough, snort. Clear your throat and choking sensation.Continue your allergy meds , decongestant, expectorant and plenty of fluids to help thin out the mucus.
Probable allergies. Since it is now two weeks and your symptoms are still present, i suspect you may well be dealing with allergies, especially this time of the year. All the symptoms you describe could be from allergies, including the throat irritation, congestion, etc. Would recommend otc non-drowsy allergy med as a trial to see if symptoms abate. If they do, talk to doc about what options are long term.