This sounds super interesting. The pills you are talking about are probiotics? Have some links to which ones you took and maybe some research you did about this?
You will know when it's restored, you can even eat garbage (meat, processed foods) and your gut will process it and move on. You should be able to notice the subtle changes when you eat something that does not digest readily. It's not the acid and body mechanics, it's mostly the bacteria giving you life by breaking down nutrients and solids. Feed it what it needs and it will sustain itself. Raw and fermented vegetables.
Humans of the past ate game meat. Very low fat, and almost all unsaturated fat. Closer to an avocado than a steak.