I am so sorry for the loss of your kittens. We are not vets here, so there is no way any of us could know what your kittens have died from. It’s so sad to hear the descriptions of their cries. More than likely, they died from something that their mother had during her pregnancy, and since kittens don’t have a fully developed immune system, the disease progresses and overtakes them. Just because a kitten isn’t showing signs of an upper respiratory infection, they can still have it.
I think if you have live kittens still, to get them back to the vet and have them checked for URI or something else. Hopefully, you don’t have other cats in your home that could be exposed to a contagious disease. That’s why it’s important to quarantine new arrivals and to make sure your clothes are changed and you have washed well before handling other cats in the house.
I will post a link for you for hand rearing kittens hoping it will help you with any remaining ones. Again, I’m so sorry. Hand rearing kittens is not for the faint of heart, it’s a hard job that has wonderful rewards, but sometimes it can be heartbreaking.
http://messybeast.com/handrear.htm