Two days later, he startled us all by screaming or crying terribly and I picked him up and he wouldn't respond and continued to scream... then he went limp on me and I thought he died right there in my arms because he wasn't breathing well and eyes rolled back in his head.
Took him to Animal Hospital right away and by the time I got him there... he was sitting up and fine. Both me and the Vet Doctor were Confused. The vet said that he might have had a sezure. After this episode, he seemed to have a runny nose and this cough now and then and it kept getting worse and would chock.
Welcome to YT
There are a lot of very knowledgeable and helpful members that will be able to offer you information as well as support. Your breeder sounds pretty questionable to say the very least. She sent you a sick puppy and whether or not the issues are genetic or not she should be helping with his medical bills. At less than 2 lbs he was entirely too small to be put onto a plane and he was also too young to have left his mother.
The above quote is the most concerning to me about your story and suggests what could be a very serious condition. Did your vet do any further testing or suggest an MRI or CT Scan? This test can help to either include or exclude several things and probably should be done. Has this happened again?
As for a replacement puppy is your breeding going to pay for the above testing to be done? If it were me I look into the Puppy Lemon Laws in your state and proceed from there. How much did you pay for him and what is your breeders name?