Sometimes it can take a little while for all the mucus to clear out. I just had H1N1 too and the whole time I was having a very unproductive cough; now, however, I am still coughing and it is more "productive." My lungs are also extremely sensitive to the cold air and going outside is enough to induce a massive coughing fit.
Anyways, my point is that it can take quite a few weeks for our bodies to get back to normal after the flu. This could also be something unrelated, as well, like a mild cold or something. The fact that you could run 3.5 miles without feeling winded is pretty impressive (hell, I don't think I could do that when I was feeling 100% at this point!) so in all honesty I don't think you have much to worry about there.
Most worrying stuff, as far as lungs go, is almost always accompanied by shortness of breath. The cold air is often enough to irritate most people's lungs, too.