First, do not take any of this as medical advice.
However, even though SNPs do not determine how your genes are expressed, there are some clues to what might be going on, and even though I can't see your gene expression, you do look like someone who can see improvement by using a methodical approach.
Your CBS mutation can lead to excess levels of ammonia, so addressing the gut (as well as limiting foods and supplements high in sulfur) is probably the first thing you should do before taking any methylation supplements as you may be a lot less likely to get anywhere.
As far as doing things like assessing gut flora (and even anti-gliadin antibodies), I really think there is no better test than the GI Effects Gastrointestinal Function Profile from Genova Diagnostics. Unlike every other other stool test, this test is extremely sensitive, and can assess and give you ranges of your good bacteria, bad bacteria, yeast/fungi as well as parasites (even ones with unknown taxonomy). This way, you can address bacteria infections and/or overgrowth, yeast/fungi, and parasites without a whole lot of guesswork. Unfortunately, what you do need, is a doctor that knows the proper way to address these microbes, fungi, and parasites - and these may be rare.
http://www.gdx.net/core/sample-reports/GI-Effects-GI-Function-SR.pdf
There is a lot to addressing the gut, and it seems that every doctor has their own approach. Dr. Yasko actually recommends using a Organic Acids Test (OAT) through Great Plains Laboratory, a Metabolic Analysis Profile (MPA), and Comprehensive Stool Analysis (CSA) through Doctor's data, along with the test I mentioned above (amongst others).
While this is extremely comprehensive, by the time you do all this testing you are set back at least a couple thousand dollars. I know I can't afford it and have not done all of these tests.
It might be best to find a really good M.D. that knows a lot about the gut or good N.D. that graduated an accredited ND school (such as Bastyr, NCNM, SCNM). Each practicioner will have their own approach.
What might be most important after addressing your gut is keeping your taurine below the 50th percentile with Urinary Amino Acids (UAA) test when starting on methylation supplements.
Looking at your results, you might have trouble tolerating methyl donors. In other words, you might have trouble tolerating supplements such as methyl B12 and folate. Considering your VDR Taq is -/-, Yasko says that there will be better tolerance for methyl donors - but I'm not sure how "better" the tolerance will be.
What sticks out to me is that your MAO-A +/+ polymorphisms and COMT +/+ polymorphisms. While an MAO-A mutation and some other mutations are quite common among the normal population, it seems that more often or not, Breakdown of neurotransmitters and catecholamines becomes quite impaired following illness, and you get stuck in a permanent state of fight/flight or may have things like panic attacks or rage attacks. MAO-A and COMT are what break down these chemicals. COMT V158M is associated with higher levels of dopamine, but VDR Taq +/+ supposedly negates this to some degree if I understand right . If you think your homozygous MAO-A mutation is causing problems symptoms associated with decreased MAO-A activity, I really don't know many great ways to address it other than relaxation techniques and things that reduce stress. Carefully addressing microbes and the gut in a way that doesn't stress your body too much may also help take the strain off of these enzymes in my experience. For myself, I find high doses of multi-strain probiotics that contain the strain Lactobacillus GG (aka Lactobacillus rhamnosus) helps calm my body as well. I have a (+/+) MAO-A as well with symptoms of dysfunction MAO-A and/or COMT enzymes.
A lot of the treatment information is based on Dr. Yasko's clinical experience rather than peer-reviewed science. I personally do not like how Yasko speaks in absolutes since gene expression is far more important than what SNPs you test homozygous or heterozygous for. And this is looking at a small number of gene SNPs, when there are many, many more that contribute to your condition.
As far as supplements - after addressing your gut and CBS, you may want hydroxy B12 instead of methyl B12. Of course, since I don't believe in absolutes, you can start with a crumb of methyl B12 too and titrate up to see if you tolerate it. You may have to start low and slow with folate as well. With CBS you may need limited intake of B6 (as P5P) as well.
As far as the other B-Vitamins, I don't really like most B-Complexes. Most are formulated bad. There are some decent active B-Complexes with Folate as L-methylfolate (Metafolin®) or Quatrefolic®. But these usually contain P5P or B6, so it is of my opinion that it would be smart to assess how you feel on each of these vitamins before grabbing a complex.
To address excess ammonia, there are various supplements that can help with that is in Yasko's book. Yucca root is one of them. While I don't have CBS, I find L-Ornithine to be quite beneficial at times. But this could be because my liver has struggled a bit over the years.
You can google "Autism: Pathways to Recovery" for Yasko's e-book.
I hope this helps a bit, and hope I didn't overwhelm you.
