Dr. Hartman,
High ammonia could come about from taurine supplementation. Also, I believe there is a taurine wasting problem with the kidneys, but cannot remember the reference for this.
The other possibility is a CBS upregulation where homocysteine is pulled aggressively towards taurine causing depletion of Methionine. I would be interested to check a serum amino acids to see how these values correlated.
The ammonia too could be gut derived from all of the dysbiosis. High protein diet may contribute too.
One area I haven’t been able to spend much time on is the Citrulline-Arginine pathway. This is another area of research that could be worthwhile. Its another layer of potential biochemical imbalance with some kids. Dr. Yasko has written about this in her material.
I cannot remember if you have done a Methylation DNA Pathway panel? I think you may have.
Dr. Woeller