First off, so sorry you are having these problems. Now, even though Wellness protein may be too high, Science Diet is a horrible food, yet vets always push it. Ask the vet what he believes is a suitable percentage of protein for your baby and/or look at what the Science Diet says and try to match that up with a more premium food. Check this site for pet food reviews:
Dog Food Reviews - Main Index - Powered by ReviewPost. Also, if you don't like what your vet has to say, see another one! Your baby is so tiny, which is usually directly correlated to higher health problems. I hope he gains a couple more pounds! Please keep us updated on his progress too.