Christine's answer is very overwhelming. Our son can't swallow pills yet, and we tried the injectable B12, but it was too much torture for all of us to do, so we gave up and went back to the oral B12. We saw a MAPS doc in our area and he tried the NuThera and he had horrible behaviors. He's on the GFCF diet which has helped his aggression and digestion.
I guess my biggest question is how do you get all this into a routine when you are constantly fighting with your child and your family to implement it?

Did you have him tested for language disorders such as Apraxia? Visual support seems to help. Hannen method helps because we struggle with social language. Floor Time seems to have more for older kids then Hannen. We are going to try DIR Floor Time. We have only used it a little.

My daughter uses sign language and PECS but within the last year her school got her a tablet that she carries everywhere she goes.

Most of the time we get her to say single words and also sign them. Since getting the tablet and her using it for a few months, the school has been getting her to use multiple words in a row. I will say they are not always clear but we know what they are.

The fact is that some children stay nonverbal or are only capable of so much. We push our daughter to use speech but we do not overdo it because she gets frustrated, we take it for what it is and keep trying and so far it is working even though it is slow.

Some kids just have a really hard time grasping spoken language. If you can add in some other things that are more in his immediate comfort zone, it may help ease some of the communication barrier. We recently had some major communication issues, and were often unable to communicate verbally for about 5 months. We used whistled tunes, clapping patterns, pictures, and I even started teaching them some sign language (that one was amazingly helpful!). Try exploring some completely alternative methods of communicating, and maybe it will help to break through that wall. Your local public library may even have some Baby Sign Language DVD's, if you wanted to look into it before deciding if it might help.

Christine, thanks for your detailed explanation and for sharing. We have tried some of the items you mentioned in the past but they could be worth revisiting. He is on a GFCFSF diet and we do limit his sugar intake as well but will look into the protocol you mentioned too.