Have you ever taken antibiotics? This can cause a gut flora imbalanace by itself and you should look at this as one of the biggest reasons for your overgrowth if you do have it.
The skin issues could be related to deficiencies in stomach acid:
The skin conditions are likely also related to toxicity and your body detoxing via the skin. If your liver becomes overburdened with toxins, it has to detox via a different method, which could be the skin or the lungs. So if you healed your liver, your skin conditions likely would improve.
There’s a lot of things you can do for your health but one vitamin has been shown the really aid your skin; vitamin C! So be sure to be taking vitamin C.
The caffeine likely drained your adrenals which is an important part of your immune system. By continuing to work out while you are trying to heal, your adrenals are continuing to be drained which prevents your body from healing if you do it too much. You should focus on your immune system and not muscle mass if you are doing the candida diet, etc.
Hope this helps!