I'd bet on pathogen die-off causing the ammonia smell. Lots of pathogens poop ammonia and they'll release even more when they die. This stuff is supposed to help mop up ammonia:
Or just tough it out, but if your blood-brain barrier is compromised ammonia can really mess with your head. Ammonia creates a more hospitable (less acidic) environment for pathogens.
Fiber helps "move things along" because it scrapes the lining of your intestines and the irritation causes mucous to be released. This is very much not what you want with IBS-D. If you need help "moving things along", increase consumption of animal fats.
If histamine isn't a problem, bone broth is awesome.
If histamine is a problem and you have the usual sinus issues give Nasalcrom spray a try. Amazing stuff. Mast cell stabilizer, not a steroid. Went OTC a while ago. It can be hard to find because the pharmaceutical mafia pushes newer prescription meds that did nothing for me.
Starving out SIBO pathogens with very low carb or Zero Carb looks like the most promising approach. SIBO can dump a lot of histamine into your system too.