Sigh...this is so complicated
Unfortunately it is complicated. Good practitioners can be invaluable in interpreting tests but they are rare. Mostly we have to stumble through ourselves.
Treat the test results as a series of potential clues to guide changes in things like diet and supplements, but in the end it will be trial and error and your own body's response that will be the final determinant.
The most outstanding results in your test do seem to be the very elevated phe and the very poor Kreb's cycle. Unfortunately the rest of the test doesn't give obvious insight into why these are going wrong.
Maybe a series of things are making small contributions rather than one big problem (though I definitely think it is worth keeping in mind the possibility of a genetic contribution to problems with PH and trying to rule this in or out).
Go through your results carefully, looking at results which are maybe normal but at either end of the range (lowish, highish), compare these with the guides, especially Rich's guide which I'm sorry I forgot initially.
This may give a bit more insight, then you are going to have to make a lot of guesses based on logic, even if test results don't particularly support it, then initiate supplement changes based on this logic and just see what happens when you try them.
For example, as we have already discussed, aconitase can be disabled by oxidative stress. On the face of it your GSH and cys levels are good, BUT serum and urine values don't necessarily reflect what is going on inside cells. A few other results could suggest there is an issue - highish lipid peroxides, lowish pyroglutamic acid (this reflects a regeneration mechanism for GSH) and lowish cystathionine (a precursor to cysteine).
The latter suggests a possible problem with B6 and or with supply of methionine and hence the methylation/folate cycle. Elevated sarcosine supports a possible problem with folate.
Other things suggest a B6 problem to me, particularly the non-existent AKG which is normally an abundant product in the cell from amino acid interconversions. B6 is tied up with B2 since active B2 is required to make active B6.
Aconitase can be blocked by nitrosative stress. This links in with the BH4 issue since it too is disabled by things like peroxynitrile.
The Kreb's cycle gives other clues about potential problems since there are several steps where metabolites feed in from outside the cycle - ie they don't entirely depend on previous steps.
We have already mentioned AKG. The next step, succinylCoA is also fed from outside, namely from oxidation of odd-chain fatty acids. Ultimately these form methylmalonylCoA which is converted to succinylCoA by the adenosylB12 dependant enzyme methylmalonyl CoA mutase. Even though your MMA marker is normal (it becomes elevated when this last enzymatic step isn't working properly), the fact that succinylCoA is virtually non-existent suggests that this step is something of an issue.
These are a few examples of how you may need to do more sleuthing. Also you will need a multi-pronged strategy.
You mentioned the possibility of digestive issues. This is something that should be addressed early - betaineHCl or dilute HCl, possibly plus pepsin should be tried, - maybe later you could think about pre and probiotics.
Anti-oxidant and anti-nitrosative strategies should be considered. Be careful with direct glutathione supplementation. Some people have benefitted but many are quite adversely affected. Precursors or indirect stimulators might be better. A well functioning methylation cycle can be important. Other mixed antioxidants might be helpful.
Martin Pall has written about nitrosative stress and come up with various strategies to address it. Unfortunately all the links I had to him no longer work, but
here is one that summarises his thinking.
Here are some of the products he developed.
Here is another link which gives a lot more background and includes thinking of others as well as Pall. Towards the end there is discussion of strategies to overcome.
Multivitamins can be misleading. We think we are getting everything but the combination might not be right for you.
You may need to reconsider your B vitamin strategy and look at individual vitamins, possibly in active form. At the very least I would urge you to try sublingual active B2 and B6. These are not expensive and worth a trial to see if they make any difference. Even though the dose per pill is relatively small they are very potent but easy enough to cut into 1/2 or 1/4s.
Folate (methylfolate is a potent peroxynitrile scavenger) and the active B12s are worth trialling also.
Here is a post I made recently on the subject.
Finally you may have something of a mineral imbalance. Magnesium and zinc are high but copper and manganese are low. Molybdenum is not measured but could also be relevant. Maybe you need to consider a balanced trace mineral preparation.
