Toenail fungus won't go away on its own, probably ever, but definitely not that fast even if it eventually does. That crap takes months to years to clear up, whatever route you take. Oh, and there doesn't seem to be any indication whatsoever that toenail fungus is affected by diet.
As to fatigue/shakes/headaches, those will continue for some time w/ a proper diet, too (IF it's actually "candida" aka some sort of intestinal fungal infestation). Have you tried anything antifungal to test for a herxheimer's reaction (die-off)? Easiest way would be massive doses of garlic. I personally wouldn't recommend garlic for treatment as it kills gut flora, too, but it's certainly a cheap and easy test substance... To eat a bunch of garlic, chop up a couple carrots, a piece of cheese, a tbsp or two of sour cream, and like 7 or 8 BIG-ASS pieces of garlic in one of those shredder-thingies (you know, that kitchen appliance that's like a blender but w/ bigger blades, whatsitsname?). Then eat it all up. If you get slight heartburn, that means nothing. If you get HORRID heartburn, you've got an ulcer. If you get major weirdness in your head, hot spells, dizziness, sweats, etc., then you've got a fungal infestation ("candida").
...if you feel nothing but bad breath, eat a breathmint, forget your low-carb diet, and start looking for another cause to your ails.