Sounds like your symptoms are tied to candida; the ones that stick out include heart palpitations, sinus issues, achiness, anxiety, and headaches. Headaches are tied to inflammation of the gut, and the gut gets inflamed by parasites and candida.
It sounds like you have a decent naturopath and I would listen to him.
Most people who have a candida overgrowth also have a parasite imbalance as well; remember if you have taken antibiotics, you destroyed your beneficial bacteria that keep both of these at bay.
There are 1000’s of parasites so I would not discount the fact that you have them; we all have them like candida, but just at different levels. They likely found a good host like the candida.
Candida is a a parasite as well.
It sounds like you had a ton more symptoms more than fatigue before your journey to health and you would likely get them all if you ate the same diet as before.
Fatigue is one of my main symptoms now after being on the diet for over a year and its getting better to the point where it is pretty much not an issue right now. I get more a fatigue as I cheat more.