J.C.
I came across a website called Welcoming Kitchen. http://welcomingkitchen.blogspot.com/
The entire website is recipes that avoid the 8 major allergens and are vegan. My son has many food allergies too and I have been experimenting with new things on here and he is loving them.
My son was also on Neocate from 6-10 months old, and I was also not sure it was really good for him, so I ended up switching him to goat's milk. I had to mix it with other things to make it like "formula" because he was under a year, but your son is old enough to drink milk, so you could try it straight. I order it from a website called vitacost.com. It is the cheapest price out there for powdered goat's milk - less than eight dollars per can and it makes a few gallons I think.
When you say he is on Neocate Jr only, do you mean he doesn't eat anything at all, just drinks Neocate? Certainly there must be some foods he can eat. With my son, we don't do a lot of "recipes" but he eats single item meals (ex. chicken, rice pasta and carrots) and he still can eat a wide variety of vegetables, fruits and meats this way. We don't give him anything processed so as to avoid all preservatives, artificial colors, flavors, etc. but he eats very well and loves to eat. The beauty of it is, if they have never eaten processed foods, they don't know what they are missing and whatever you offer to them will be new and hopefully tasty. You should be able to get away with this for a while longer, until they start wanting what other kids are eating.
Good luck with this. I know it can be really tough. You can contact me if you would like any more help.