Oh dear! You must be sick with worry! My son was also really sick when he was about two. He had a bad cough from November all the way through January. It kept him, and me, up at night. I think there was some stomach flu in there too at some point.
Here's what happened. After weeks of complaining to the doctor on the phone and bringing him in to check what was going on the doctor perscribed a Flovent inhaler. I had been giving my son Albuterol liquid, and had already switched to an Albuterol inhaler. (The Albuterol just made him crazy.) The Flovent started working very quickly. In about a week his coughing had subsided. He still takes it twice a day and it keeps the asthma at bay.
Next, I switched to all organic food and natural cleaning products (like 7th generation or method, both of which you can purchase at Target) This probably sounds crazy, but I think my son was alergic to pesticides. Both my children started feeling better; their asthma and allergies decreased, colds stopped coming on monthly and their immunity was all around much better.
Finally I also switched to heatlh food store brands of vitamens for both kids. There is an immunity gummy bear vitamen sold at Whole Foods that includes echinacia, vitamen C, and Zinc. The same company also makes echinacia lolipops. They aren't cheap, but they really help during cold season.
I doubt any of these things will help overnight, but they will help in the long run! Good luck! I hope your little one gets better as the weather improves.
H.