
I unfortunately I have been down this road far to often regarding vaccinations :(
I am not going to give my personal opinion on vaccs but if I were you, I would definitely change vets and do it TODAY. Get the new vet to do a thorough examination of your pup and explain all of the symptoms and circumstances. You can't take
any chances with one so young. Especially since you have had a very unfortunate experience in the past.
Regarding the sour smell, in my experience, all unwell dogs give off an odour. My latest pup, after having a very bad reaction with vaccines gave off a sour "metalic" smell, and until I got all of the poison out of her system, continued to smell this way.
But please get your pup checked out as they can go down hill very quickly, especially in view of the fact your pup has had to cope with very different circumstances, ie, new home, stressful journey and then vaccinations that it probably shouldn't have had so soon, all this weakens the immune system.
Let us know how you get on and good luck :)