One thing that can be the problem is that your air is very nasty which causes you to have a lot of problems with it. I understand how it can happen at night because your body is trying to relax and take as many of its systems off-line so that it can generally rest. This said, if your air is bad than your body will then be ingesting more of these harmful particles. I can probably guess that your air is bad, and it's mostly a matter of airflow, but most all homes have air that is quite significantly worse than even the worst of outside environments. Therefore, what I would suggest is getting an air filter for your entire home such as what I have.
I used to have problems with my air, but after a colleague of mine talked about Polarized Media Filters I decided to try it. I did research on it and found that it would be well worth my time, and after I got it I was very pleased with the results as I no longer have problems with my air. It's a filter that goes on your furnace and thus uses the air system that is already in place for heating. It then creates a static field that attracts the particles to the fibers of the filter. It is a very efficient system by all accounts.
The best place for price that I've found is at www.airlifeone.com. I'd further recommend the Electrobreeze brand as it is cheaper than the other but is essentially the same product.
I hope that this helps.
Strep Throat? Sinus Infection? I'd get to the doctor - mostly because it's been a week! Bronchitis can also be the culprit. Sounds like there is fluid draining down your throat from sinus that keeps you up and coughing...
Get to a Doc... good luck!