I am glad you are trying the diet both for GERD and potentially related respiratory issues. I can’t comment specifically on your case, but here are a couple of thoughts on the general topic. I would recommend anyone with symptoms including shortness of breath and fever to remain under the care of a doctor just to be sure there is nothing more serious going on.
The connection between GERD and asthma is very strong. It’s clear to me that something in reflux other than stomach acid (Refer to blog article on this site, particularly the SARA study) is exacerbating asthma. Whether that is enzymes, bacteria, bile or something else might not matter because stopping the reflux should eliminate, or significantly reduce any and all of the asthma triggers linked to reflux.
Studies in asthmatics following fundoplication operations (known to control reflux in 90% of GERD patients) show that there is definite improvement in GERD and asthma symptoms as well as reduced asthma medicine usage when reflux is controlled. Pulmonary function, on the other hand is less responsive to the surgery. Perhaps pulmonary function may improve over time, but longer term follow up studies might be needed to fully answer this question. Here are some links to studies on this subject.
Please do share your progress on the Fast Tract Diet here.