What else are you eating? If you don’t have any carbs in your diet then the protein spares your body from destroying itself, which probably makes you feel a bit better. Maybe some of the vitamins like B12 gave you a boost too. If you aim for at least 50g each of carbs/protein, you can avoid the body destructo thing, unless you’re especially active.
The ammonia issue is more complicated than I understand. Your body turns over 300-400g of protein a day. What you eat just helps to keep the body’s stores topped up so it can maintain these processes. Ammonia might be created if you eat more protein than you need as the body discards it, or during processes like gluconeogenesis (try smelling the breath/pee of someone on Atkins). Meat is partly digested by bacteria, which is why you can end up with ammonia in the gut. I’ve got no idea how it’s processed from there. Usually it’s converted to urea, but maybe it’s allowed to pass in the stool.
Gelatine and bone broths are good sources of additional protein that don’t putrefy in the gut. Kefir is a good source too, but large amounts of lactate might be an issue with low-carb intake. I’ve seen a study showing omnivores having a lower stool pH than vegetarians, and they strangely ate more complex carbs, so perhaps this suggests balance is key – there are even some beneficial bacteria that feed on the grisly parts of meat.