It sounds like a total gut ecology issue, and it would take longer than two weeks of ZC to mend.
There are a number of things that could be done, I would recommend intermittent fasting, perhaps start with a 3 day water fast....see if there are improvements with that....then reintroduce foods slowly...and remember quality maters. Start off real bland, with Raw meats, animal fats, leafy greens...ZC may not be the best way to go, so consider low carb for a period of time, and perhaps even a follow up intermittent fast. The old gut ecology needs to be cleared away and a new one built up with more optimal raw materials, its a process and it will take time.
Healing is a lifestyle so other issues must be dealt with, getting rid of drugs, medications, supplementation is also really important, so is eliminating stress.
Find time for relaxation, and I highly recommend regular sunbathing. Dont look for any quick fixes, it can take a couple of years to fully re-balance after antibiotics, even in ideal circumstances.
Get away from the idea that its a bacterial issue...bacteria overgrowth's are symptomatic of a greater systemic imbalance or toxicity....this will not be addressed mainstream mainstream methods...and even so called integrated medicine is somewhat dubious in their recommendations. Let thy food by thy medicine
Its difficult to give any real detailed recommendations second hand because there is no way of knowing, also there may be a reluctance by many to eliminate all their food intake for days at a time and come off a fast eating raw stomach smoothies, blood, and organ meats.