We had him vaccinated w/bordatella when he was only 8wks old cuz he came to me from his breeder already sick w/kennel cough. He suffered through it for 3 months. The only thing that worked was upping the dose of antibiotics (Clavamox) to 5ml from 1ml.
We did 3 rounds of antibiotics, many medications including Hydrocodone, 3 different vets & 1 specialist because an x-ray indicated that he had an enlarged heart.
He had an echocardiogram, it's like a sonogram of the heart. According to that test, he was ok.
I didn't read through all the posts of the op, but I hope your baby has a speedy recovery.