Choosy, Picky Eater. How do I Get Past This Hurdle?

I am seeking some help and some advice. 

My road so far on the Autism journey with my preliminary diagnosed son has not been to rough or nightmarish as I sometimes read on other blogs. Logan has been pretty well behaved. He is developmentally delayed (severe) but that can be handled. He does have a meltdown or two here and there and that is handled. The one thing that has me worried at the moment is his nutrition and eating habits. I know it is common in autistic children to be choosy eaters but how far should I let this go. 

Logan once enjoyed many different types of foods when he was an infant. He would eat all the fruits, vegetables and even the baby cereal (the first of my three children). As he got older the pickier he got. Just a few months ago he would eat rice chex soaked in milk, bananas, vanilla wafers, scrambled eggs, chicken nuggets, french fries, carrots and one of his most favorites was grilled cheese. Not to bad for an autistic child right? I did not have many worries about his diet at this time. 

Logan started school and became sick ALOT!! I addressed the issue of his eating habits to his doctor because they had gotten worse and less foods. He advised us to put him on pediasure to try to make sure he got some of the nutrients he needed. It got to where he could not hold any of this down and started throwing up almost every day or night. 

We took him to the doctor and I requested allergy test for milk. His doctor tried to do a whole food panel test. Unfortunately they could not get enough blood to test for everything but did get enough to test for cows milk allergy. Sure enough my poor son is allergic so there goes even more things from his diet that he can not have. My son now only eats bread which I have to get a special white wheat kind with no milk, crackers, shortbread cookies because he can no longer have his beloved vanilla wafers. Everything else I seem to try he refuses. 

His therapists at school they will try to do it some during his lunch time to try to work on eating habits. My son is one month away from two and hardly eats a thing. He is not losing weight yet but the thought is in the back of my mind and scares me. He no longer sleeps through the night. Ever! I want to put the blame on him possibly being hungry. How am I to know though? As I have mentioned before Logan is non-verbal. Sign language is being worked on at school as well as in the home but he has yet to really utilize any of them. 

Since finding out his milk allergy his eczema has improved enormously!! The downside, his diet is more limited and soy milk seems to go right through him and he does not get as full so it means for a more restless night. Something has got to give, there has to be something out there that he will like. I am yearning for a full nights sleep because my sons belly is finally full. I want my son to be healthy and the threat of gastrostomy tube to be out of the picture all together. If anyone out there has some advice I welcome it!!!

Logan enjoying a hash brown after having tubes put in his ears. He did eat 3/4 of it :-)