Hi J. - my son who just turned 3 has a history much like your daughters. He has struggled with many awful coughs and runny noses. We've tried modifying his diet but it made no difference. Finally doc finally prescribed a round of Amoxicillin and his nose and cough are almost completely clear.
I struggle with asthma and allergies so I have some personal experience with this. I caught the same bug my son did in March and it was awful and hung on forever. My asthma doc changed my inhaler and the cough cleared up immediately. He said I had some residual inflammation that was causing the problems.
I would definitely consider taking your daughter to be evaluated by your pediatrician and possibly an asthma/allergy specialist. It may or may not be an infection like my sons. She definitely has inflammation in her airways - the new symptoms could be a seasonal allergy or even a new cold that make her breathing symptoms worse. With my son, we decided that if the antibiotic didnt help, our next step was the asthma/allergy specialist.
Be sure to talk to your doctor about what OTC stuff you're giving her and he can help you evaluate what will work best for her and give you dosing instructions based on her age and weight. OTC cough and cold medicines are contraindicated in kids as young as your daughter. I was giving my son Sudafed but my doc recommended Mucinex for Kids instead. It was far more effective. Steaming in the bathroom, a humidifier at night work wonders for congestion. Honey works great for dry cough. Cleaning her environment, reducing exposure, washing her hair every night, keeping shoes and dirty clothes outside of the bedroom, and bedding washed in hot water will help if it's allergies.
With some expert advice, I can imagine your daughter will be feeling better in no time!