I'm barking up the wrong tree altogether, and perhaps, dragging the doctor along with me. There are no ketones on his breath; there never were. I finally found some descriptions of "ketone breath" - fruity, like a pineapple crossed with nail polish. That's not even in the ballpark! I went down the ketone path because I smelled it on Wendy's breath, on her low carb diet, but no matter, it's not ketones. There's nothing wrong with John's Krebb's cycle, and that's good news I suppose, since a genetic defect in this area would be near-impossible to fix. (He'd probably be dead anyways.)
I keep going back to stale beer; that's the key. I return to google, and discover some articles on "light struck" beer, where the hops interaacts with light to produce <mercaptans>, chemicals which are also employed by our friend the skunk. These are short hydrocarbon chains with an SH (rather than an OH) at the end. Crotyl Mercaptan is definitely <on the list>.
Where are we now?
In 12 years of marriage, Wendy has produced mercaptans only twice, on the low carb diet. Why? Lots of protein containing sulfur amino acids, and not enough water. Could be a harmless form of bad breath, sent in a different direction by the change in diet. It could mean absolutely nothing!
But it means something in John's case, or at least it use to. Remember, I smelled the mercaptan on his skin. Not often, but I did, once or twice. Not the onion/garlic smell that sometimes ekes out of my pores, but the mercaptan of stale beer. It wasn't oral bacteria, not simply "bad breath"; the chemical was in his blood stream, and probably in his brain. It's being made somewhere else, somewhere inside. There is a bacteria somewhere, and if we feed it cysteine and methionine, it produces mercaptans. If we feed it anything, it creates toxins that resemble or derail neurotransmitters. Where does this bacteria live, and why can't we see it? Must we starve it into submission, or can we kill it with an antibiotic? I don't know. One thing's sure; only a bacteria can make that smell. A human, even a genetically flawed human, lacks the necessary enzymes. We are chasing a microbe.
I'm pretty sure this microbe, troublesome as it is, represents an opportunistic infection. Something else went wrong first, then the microbe moved in, or evolved. Some of the tests are back, and the amino acids are off. Three of them are too high, and three are too low. This is trying to tell us something, but what? I believe it indicates a metabolic disorder of some sort, a genetic deficiency, and perhaps a bacteria has learned to make a living on the novel metabolites, making John's disorder ten times worse than it otherwise would be.