It's mold in your home! I have had the same symptoms for months every summer, including: swollen lymph nodes, itching, metallic taste in mouth, breathing problems, excess clear phlegm. I looked up mold symptoms because my home has an iffy sewer line, and floods occasionally into my finished basement and I was amazed how many things I hadn't even noticed, but we're a problem, confusion, memory issues, lethargy. I'm tearing out the drywall tomorrow and treating with Concrobium from home depot. Look for mold! Anything leaking, previous flooding... especially in drywall, it gets inside and you might not even see it! They sell home mold tests that don't cost that much! Good luck!
Pertussis (whooping cough) has been on the rise for years now though few doctors acknowledge this fact.
I'm not a doctor, but if I were you, I would take your sons positive whooping cough results to a specialist and ask that your son be treated for such while they look for other possible causes. (Doxycycline is the antibiotic of choice along with some short term steriods)
Although I repeatedly asked about whooping cough, my father and I were misdiagnosed for 3 months until I fractured my ribs in several places from it. Even then, it was my dogs Veterinarian that suggested the steriods (I took my dogs prescribed prednisone) that finally cleared it up. Before my dx, I saw numberous doctors and I was also put on asthma meds and various antibiotics, excluding Doxycycline, to no avail. My lung function decreased as your sons has, I had periodic wheezing and I had normal x-rays. It's usually a self limiting disease in older children and adults with little chance of complications, but its course is extremely miserable. Because of my lack of diagnosis in the begining, it took me almost a year to recover fully.
Best wishes!
You should try posting your question at the Respiratory Forum. Good luck!