Kenna, I also have the morning cough that I guess I assumed most CF people have. When I've just finished a round of antibiotics I will generally have a few weeks with a lot less mucus and it's such a gift. Then it starts generating again to the amount where the morning cough returns and increases as time goes by. Right now, I average 45 minutes and 1/3 c. of mucus every morning which starts a couple minutes after getting out of bed. Everything settles while laying down during the night and then triggers the cough to clear it out when I stand up straight; once it starts, it has a mind of its own.
For me, I just keep moving forward through my "first thing in the morning" routine, pausing to cough and spit (pretty). I try to keep my mind active and on other things while I'm making coffee, checking blood sugar, shooting insulin, making my breakfast, dog breakfast, dog medication, etc. By the time I take my pooch out the cough has usually started to settle down. I eat breakfast, check email... and then it's time for treatments... and more coughing. And sometimes I actually stop and ask myself, "why am I so tired?" Really?
So, I guess in answer to your question--re. motivation--I would say having a routine to keep my mind on throughout the coughing portion of the morning helps me; and, as other people mentioned, having a daily non-CF routine that needs to be followed, which includes things that you enjoy. I know when I have work or someplace I need to be, a project that needs finishing, lunch date with a friend... it takes my mind off the "daily grind" of the disease and trumps the CF symptoms. Having a purpose really does help.