Momo was sick for 3 months after his Bordatella shot when he was a pup. He was on 3 rounds of antibiotics, what finally worked was upping the dose to 1ml from .3ml. But that caused his stomach irritations, it's important to give them probiotics, like yogurt.
A note about the x-rays. Yorkies have a large heart shadow that appears in the x-rays. Some inexperienced vets might diagnose him w/an enlarged heart (that's what happened to me & Momo). If his heart sounds ok, don't be alarmed. I spent hundreds of $ on an echocardiogram bc of the above, when everything was ok.