Oh gosh this doesnt sound good. I see LS has been ruled out..
Is her head shaped funny kinda like domed? Maybe hydrocephelus (water on the brain)
THe cough? Collapsing treacha?
Is she falling over alot? Like unsteady on her feet? (atlantoaxial instability)
Im not a vet just throwing some common yorkie things out there
Whatever is going on I would get a second opinion from a different vet.
Whatever you do please dont return her to the petshop (beleive it or not alot of people do because they dont know what else to do for their puppy)
All they will do is probably resell her and the next person will be dealing with the same issues as you.
I pray you find something to help her quickly. I wish I had some advise to offer that may help but I dont
