It's good that want to get to the root cause and that you see modafinil more as a temporary solution, rather than something to rely on long-term. I've struggled with chronic fatigue, brain fog, ADHD, digestion issues and anxiety all my life until I changed my diet and lifestyle. 
Eliminating damaging foods and products, incorporating healthy nutrient rich foods, incorporating detox foods and supplements that especially detox heavy metals and virusses were key in changing my health.
Eliminating damaging foods:
Eggs All animal products Soy Corn Dairy Gluten MSG Processed foods Citrus acid Vinegar Incorporating healthy foods and habits:
Lemon water 16 Oz upon waking up Drinking 16 oz celery juice after 15-30 minutes  Drinking a smoothie with detoxing ingredients 1 Banana 1 cup Orange juice Frozen red berries 2 cups of (frozen) Wild blueberries (wild is important) Handful fresh cilantro 1 ts barley grass juice extract powder 1 ts hawaiian spirulina 1 ts dulse flakes or powder (If you can stand the taste) flax seeds for omega 3 Filtered water Limit fats for a while for enhancing detoxification (Ideally all fats) Limitting fats also means limitting protein -) most protein sources contain high fat Limit salt (ideally remove it for a while) Consume high quality vegan protein powder daily For the rest, eat mostly healthy carbs like fruits, vegestables and herbs. Look at the link below for dinner and lunch ideas ideally buy organic stuff, but conventional is ok If juicing, buy a slow juicer instead of high speed -) more vitamins and minerals and more juice/less product -) less expensive long term Drink a lot of water Supplements that were helpful in my healing was:
B complex (b12 as methylcobalamin) Zinc sulfate liquid Magnesium glycinate D3 Lemon balm Ginko biloba EPA & DHA (Plant based) Ester-C Melatonin Most of these recommendations follow medical medium guidelines. On his website, you can find recipes for dinner and lunch that follow the guidelines. It's when I started this strict diet, I've noticed my energy increased dramatically. Instead of feeling weak, tired, brain fogged, I started feeling motivated, sharp and had tons of energy. I suggest trying this strict diet for atleast 3 months and then see how you feel. If you want to be more flexible, by all means add some variety, it's not meant to make you feel bad because it's so strict. Just for the 3 months, be strict with it because you want to allow the body to have the maximum ability to heal and have all factors in place for getting rid of all the heavy metals from the deepest parts of your tissue. 
https://www.medicalmedium.com/medical-medium-blog-recipes.htm