I never suffered with shortness of breath while I smoked, but I quit three days ago and am now really short on breath now. What's going on?

Common occurance. It is fairly common to experience shortness of breath and cough after you quit smoking. Sometimes, this can last 4-6 weeks. If it lasts longer then that, then consult your physician.
See doctor... You should see your doctor since shortness of breath can be a life-threatening symptom. If it is severe, go to the er for evaluation and treatment. There are treatable reasons for this including bronchospasm, gerd, sinus problems, etc. You may need pulmonary function testing for diagnosis. So, see your doctor for diagnosis and treatment.