The timeframe varies person to person. For me stage 1 lasted 6-12 months because I had a heavy infestation and was very serious. However I still smoked cigarrettes which was pretty dumb (I have now quit for 5 weeks now finally after all of this time!)
So plan on a few months…
Another thing to consider with the weight lifting is to reduce how much you do it. You need to focus on healing your immune system and not building muscle. You might get too drained continuing to do that on the diet…
For your protein needs I would look at RAW almond butter instead of roasted. The stuff in the containers does stay fresh and doesn’t build up mold, so don’t worry. I made a bad statement about that on some of my threads and I now think its fine in the container. Its still best to make it from the machines, but go with raw almond butter for all of the nutrition benefits.
I would also look at making smoothies to address your nutrition needs. Grind up some healthy stuff like kale and other veggies, nuts, etc. and its a good way to help give your digestive system a break.
One other thing to check out is teff flour. Teff is similar to wheat but has no gluten. It has great nutritional properties, its a hidden super food item basically. Tons of prebiotics and a few hundred strains of bacteria are found within it. You can even make kefir teff bread somehow.