My baby sounds just like yours. Except he did not have to go to the hospital. His choking never got that bad. He is just fine now, but for the first month he was super cranky, spit up constantly, choked, etc. Our doctor said it is common for babies to do that and it will peak at 6 weeks, and either go away, or if it continues, then they would consider testing for acid reflux. Anyway, all his symptoms, except for occasional spitting up, went completely away within one week of me cutting out all problem foods from my diet. I am personally allergic to wheat (BTW, spelt is a form of wheat, so truly allergic individuals CANNOT eat spelt as a substitute for wheat). I cut out all dairy, citrus, tomatoes, broccoli, cauliflower, chocolate, coffee, caffine, soy, peanuts, eggs, and seafood. I ate a lot of green salads, beef, and brown rice. It was SO AMAZING, the difference in him! It was like night and day. He turned into a happy baby.
I had the flu once when he was about 6 or 7 weeks old, and I did NOT feel like nursing, I was SO SICK, so my hubby gave him a bottle of formula. He broke out in a pimply rash and was super cranky and got REALLY congested from it. A few days later, I ate some cheese, and sure enough, the same thing happened. Anyway, long story short, he's sensitive to dairy. So maybe you could try eliminating that. But anything you eliminate, give it two weeks to get out of your (and his) system.
Now I can eat anything except dairy and he's fine.