How do I fix the trust and relationship with my puppy again

So.. heres the story. I live in Brazil with my wife and son and at one night we heard a puppy crying horribly from outside in the middle of the night, we went outside and saw that he was very small.. my guess is around a month old. I couldn't just leave him so we took him in. Kept him warm, fed him and let him rest. The next day we took him to the vet for worm medicine and a full check-up and when we looked in his small blue eyes…we decided to keep him, so we gave him a chip and a name "Bobby". We took him home being happy with the decision that we now finally have a dog… I never had a dog in my life, not that I don't like dogs but I used to very allergic to them but as it seems i have outgrown my allergy.

Few days go by and I then found out it is not easy having a pup, especially a stray.. god knows what trauma's he has. He cries almost the entire night, eats the paint from the wall and goes insane after we feed him like it is his last meal(I looked this up and this seems to be a survival meganism) we didn't know how to calm him down so we let him sleep in our bed for a few nights(i know its bad) now he wants nothing else but sleeping in our bed and again cries the whole night… we are both exhausted and I truly want to understand what he wants.. if i'd understand i would give it to him. Now this is no excuse but after this was constantly happening.. I snapped, I didn't hit him or anything but I grabbed him firmly and yelled, multiple times.. I feel like the most horrible person in the world because I think he is now scared of me, he ducks under the bed and he doesn't let me pet him anymore.. he does eat from my hand but I think that's just because he loves food, he won't really allow me to pick him up and cuddle him he just softly bites me and starts moving around indicating he wants to be put down.

My son is 2 years old and of course I correct him all the time but he is still a bit clumsy with dogs because he thinks its a toy so he hurt Bobby accidentally a few times too.

I also want to add that after he gets food he goes berserk, he cries, his heartrate is super fast and it seems like he just wants more and more and its very hard to calm him down do I just ignore him?

I now feel we are like a terrible family to him and I want to make him feel safe and loved but now he just hides under the bed most of the times. Please give me some advice on how I can improve myself as a dog-owner and how I can regain his trust and love and make him approach me again.