Are you having die off like symptoms even before starting the anti-fungal protocol?
A low carb candida diet is intended to starve candida but nourish you. However, sometimes we feel a bit worse before we feel better. When symptoms of headache, fatigue, irritability, aches/pains etc. occurs shortly after starting the diet, this may be "die off".
Though die off from diet alone is not as radical as from the use of anti-fungals, starving the yeast of their usual nutrient sources cause some of them to die off, causing some of the above symptoms.
It is possible, depending on how heavily you relied on carbohydrates and sugars before your diet shift, that your new diet may have triggered a sort of allergic, addictive withdrawal from sugar and other indulgences. You could also be withdrawing from coffee. And/or it is also possible you are relying too much on protein foods. Eating too much protein can cause some of the same symptoms.
Another very likely explanation for at least some of the symptoms is the rapid shift to a very low carb diet which requires an adjustment in our metabolism. Most of us (unless we have been living a hunter-gatherer lifestyle), are accustomed to glucose from carbohydrates as our main source of energy. When we switch to low carbohydrate, the body must learn to use either protein or fat, neither of which it is very practiced at burning for fuel.
Ideally we replace carbohydrate intake with fat intake (only recommended after largely removing sugars and concentrated carbohydrates). Fats are a cleaner, more efficient fuel for the body than protein and eating them gradually trains our body to burn fat so that it can also make due with our own body fat when we need to (a state called ketosis).
The high healthy-fat, low carb diet recommended by brain specialist, Dr Permutter and an increasing number of other doctors, recommend that as much as 70% of your calories from healthy fats and oils from organically raised pasture fed butter/ghee, coconut butter, healthy cold pressed plant oils, and fat from pasture raised animals.
But even with the healthiest fats, if our body is not accustomed to burning it for fuel, we may feel fatigue and some of her other symptoms mentioned above. If you are feeling symptoms following your diet change only (no anti-fungal involved), you might be experiencing what is called keto flu (named after the metabolic state of burning fat which is called ketosis, a safe, healthy state but foreign to many of us).
If you think it might be your metabolism struggling with a change in fuel source, you can try a couple of things that might help you determine if this is the case. If taking remedies known to soothe keto flu help, then you will have your answer.
Certain minerals and foods can reduce symptoms of the 'keto flu' though they do not not always eliminate it. When first adjusting to a low carb diet, our bodies can start releasing sodium and fluids and this can cause us to feel dehydrated and tired. As long as you are not struggling with heart disease or high blood pressure you could try adding some extra unrefined sea salt to your next meal (some recommend taking about 2 grams more per day than you're used to). Taking sea salt 'reminds' the body to hold onto some more and it helps with electorate balance.
Drinking a large glass of water could help as well. Also, consuming electrolytes from long simmered bone broth, Mt Capra goat whey mineral matrix, coconut water, or miso soup can help. Finally, taking extra magnesium can be very important. The pure Bisglycinate form (i.e. CanPrev Magnesium 80) is less likely to be laxative. If you feel better doing any of these (except drinking water only), your symptoms may have come from the Keto flu more than from die off.
PS For more info, you may also wish to read the post about Die Off .