Hi,
Sorry to hear your puppy is not well. I have a 6 month old little girl Wei named chloe. She too was on Bonnie puppy dry food when we got her. We soon changed her food over to a better quality dry food which we did gradually as the Wei's seem to have sensitive stomaches. I would probably take the puppy to the vet just to eliminate any serious issues.
From my experience so far any sudden change in food results in an upset stomache so if I'm going to alter chloes diet I do it gradually over a few days. Just on the vaccination issue, Chloe didn't react at all to her second vaccination however the third one was a different story. The vet used the same brand and type of vaccination as the second but Chloe reacted quite badly e.g. couldn't open her eyes due to swelling and sensitivity to light and her face and throat began to swell. That resulted in a 1am trip to the animal hospital and an antihistamine injection. I have now been advised to get an antihistamine injection with every vaccination as a precaution.
I hope he starts to feel better soon.
Amy.