So sorry you have the flu! Pretty sure I had it this year and my daughter with CF too even though we all get the flu shot. We did not get swabbed but We had all the symptoms, fever, sore throat, cough, I (don't even have CF) and I coughed up a couple mucus plugs.
Drink as much fluids as you can! Gatorade was our friend. Do you have someone to do manual CPT on you? Sometimes that can help focus on certain areas.
My daughter with CF ended up on Prednisone, cipro, Zyvox and TOBI...It took her a long time to get better..WE did treatments every 4 hours. Lots of rest, lots of probiotics, deep breathing exersizes. Chicken soup, eat anything you can tolerate...Motrin and Tylenol for fever.
Do not hesitate to call your CF doc if something doesn't feel right. I think I spoke with my daughter CF doc at least once a week , if not more when she was sick.