I too am sorry to hear about the loss of your pup.
So, if I am reading this correctly, the pup you have now is just shy of two months old?
Were the puppies dewormed yet? I know it sounds weird, but both hookworms and roundworms migrate through the lungs at points in their development. Severe infestations might cause symptoms like these. Did the pup have any tarry stool before he died? Has your veterinarian run fecal samples yet?
I would also consider posting this question in the Ask A Vet forum. There is a special pregnancy and pediatrics section there that could be helpful to you.
I am so sorry you lost your little pup like this. It's doubly sad I think, when a little one goes, who has hardly had a chance at life.
It's very strange that the vet can find nothing wrong. I don't really know what could be causing this. And I don't know anything about canine asthma.
But I can tell you that very occasionally, my dog has what I call a 'funny turn'....she has had it all her life. My vet was stumped, and after examining her thoroughly, concluded it was probably either what is called 'reverse sneezing' or something nervous in origin, which doesn't have a pathological cause. She does exactly as you have described with your second pup. She seems to 'catch her breath' for a few seconds, looks scared, comes to me for affection. I gently stroke her, talk to her in a normal voice gently, and say positive things, and she is fine in about a minute, with no recurrence, until the next time (which might be a year or 18 months later!)
This really worried me the first time it happened. I tried to work out what might have caused it, but couldn't identify anything. Now, if or when it happens, I know it will pass in a couple of minutes, and she'll be fine.
(My dog by the way is healthy and fit, passed all her blood panel and urine tests last week, has no health issues, eats and sleeps well, etc.)
This reminds me of something that used to happen to me occasionally when I was younger. I would wake suddenly in the night,(half asleep and half awake) think I was choking, catch my breath, sit up, feel scared, and be just fine in 2 minutes! And I have no health issues. I always thought it was some kind of nervous spasm. It doesn't seem to happen anymore.
Of course, what I've just said about myself and my dog doesn't have to be the same story as what is happening with your pup. I would say that if it keeps recurring, take her in again for the vet to run some fresh tests. If it happens very frequently, there has to be a cause. It is up to them to find out what.