In the healthy lung there are small hair-like projections called
cilia that clean the lungs by moving mucus up and out. Smoking paralyzes this cleaning system. Each time you quit smoking your lungs begin to recover from the inflammation caused by the smoking abuse. Most likely this inflammation is causing your symptoms. Coughing up mucus is a good sign. It shows that this cleaning system is working again. When you were smoking this mucus would just stay in your lungs. As long as you have quit smoking before there has been permanent damage to your lungs then you will get better as the cleaning system cleans your lungs. This may take up to a year after you stop smoking.
We all breathe really shallow in our sleep. What you experience in the morning is probably small areas of your lung re-expanding after they have collapsed during the night. This suggests that your lungs may be sensitive to the smoke. Thus your lungs are more likely to develop chronic obstructive pulmonary disease (COPD) or emphysema over time.
At this time quitting smoking is the most important thing that you can do for yourself! Congratulations, you have made a wise decision to stop smoking! You may want to look at our Quit Smoking Topic Center at http://www.nationaljewish.org/topic/smoking_cessation.html for ways to help you kick the habit and smoke no more.