I'm so sorry to hear about this. I can relate. I have a 6 year old nephew with Asbergers. He lived with me for many years, so he is like my son. His mother doesn't want anything to do with any 'natural' methods of healing. I suppose when he gets old enough, she will put him on meds and I cringe at that thought. I snuck a drop of MMS into him a couple of times just to see if it would help. Both times, I IMMEDIATLY saw a difference in his eye contact and focus.
My advice would be as others have said, keep focusing on your own healing, and, is it ever possible to get custody of him? if you had fulltime custody and she had visit on the week-end let's say, at least you would be able to implement the protocols and diet changes the MAJORITY of the time, even if she is not onboard and doesn't follow through when she sees him. I know that is drastic, but it's just a thought.
Or what about having him for a 6 month period and doing all the diet changes and protocols and once she sees the difference in him, she will change her mind? I've often thought about that with my nephew. Telling my sis, I will take him for 6 months, implementing some stuff, and then once she sees the difference, she would be onboard with it, too.
These are just some thoughts. PLease keep sharing.