Oh, I feel your pain as I felt the exact same way when I started! It can be very confusing, especially the supplements. What you're doing sounds great
I can't remember what Missing Link has in it, does it have Omega 3 & 6 and digestive enzymes? If so, then you're good. I also give yogurt, cottage cheese, boiled egg and fruit for snacks to help balance things out even more. I wouldn't worry about going grain-free unless your little one has allergies.