Ammonia when eating meat sound like low stomach acid. Consider B12 and perhaps B6 and folic acid, as they go together. Intestinal overgrowth also comes to mind. Sulfuric foods like garlic and onions help absorb iron and copper, and if used wisely, can have an antibiotic effect.
Inability to digest fat sounds like a bile issue. Supplementing taurine may be wise, as it needed for bile production and is an amino acid abundant in meat, which it sounds like you can't break down right now. Bile also cleans the intestine, so if it's lacking could be a factor in your digestive difficulties.
While I know nothing about iridoglogy, bile is yellowish-green and I would lean towards that rather than copper.