Misty, first of all are you sure it’s not whooping cough? It seems a long time for a cough to linger around.
Aside from that, there is a peroxide/humidifier protocol we use recommended by a ND which works well for colds/flu and respiritory issues. It does not dye your hair or your bedsheets which might be a common concern! 
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Hydrogen Peroxide Sinus and Respiratory Protocol
Mix one pint of 3% Hydrogen Peroxide with two pints of filtered water.
To run the humidifier all night, mix two pints of Hydrogen Peroxide with four pints of water. If someone is more reactive, then use only 1/2 – 1 pint of Hydrogen to 3 – 3/12 pints of water.
Place the solution in a COLD-WATER (cool-mist) humidifier. Steamers will not work.
Breathe deeply from the mist stream.
Then sleep with the humidifier running in the bedroom.
Keep windows and doors closed.
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Also, what about your vitamin D levels? It’s been shown that lower D levels in people leave them a higher risk for respiritory illness and flu. I know that cod liver oil is the best way to up your levels, but personally I can’t take it. My kids will, go figure, but I can’t choke it down. I use D3 – 5000 mg per day.
I hope this helps and that you all get to feeling better soon!