The important thing is that this puppy is doing well. The origin of his illness may never be known. Many dogs thrive on raw, just as many on commercial food, some do well on Ole Roy. I had a dog make it to 23 eating only Burger Bits.
If he gets sick again, then try to determine the source. Feed him a brand name kibble, keep him trim, give him plenty of fresh air and exercise, and continue to do the best you know how. In return he will do as well as his genes allow.
IMO TOTW is a very good dog food. I've fed it to several of my dogs and they did well. I've also had many dogs live well past 12 years of age eating only a locally milled dog food that was mostly corn. Recently I lost a 151/2 year old that ate Purina all of her life. Most of my dogs never saw a vet for being sick and they did not eat raw or expensive food like Origen. It's in the genes, baby.