Having lived in Japan for a year myself I firstly would like to say.. Why would you go to Japan?? I felt like I was dying in Japan, in a very real and literal sense. If you're only there for a short vacation, it won't be that bad. But I'm sure your candida will be much worse due to the lack of quality and scarcity of food in Japan.
Everything is LOADED with Mono-Sodium-Glutamat (Natrium Glutamat) in Japan unless you cook your own food from scratch. Ramen, gyoza, tonkatsu, curry, sushi, hamburgers, omelettes, etc. I never had blood pressure issues but mine went through the roof in Japan. I knew several foreigners in Japan that were advised to leave the country by the doctor because their high blood pressure and dizzy spells got so bad and they couldn't diagnose anything.
As for soy sauce, it should be the least of your worries. Soy sauce is fermented, so it won't be that bad. Just know that every dish that has soy sauce at a restaurant or convenience store also has many other more harmful ingredients.
Japanese alcohol is straight up disgusting. All of my alcohol was imported. Do not under any condition drink any of the fruity alcoholic beverages in Japan, they are the worst lol.
There are no real organic food stores, although you can find very few small specialty food stores (literally around 6 in all of Tokyo) that have some organic foods at a ridiculous price. One is called Natural House. I used to get apples for around $6 (USD) each there. Some of the regular grocery stores have apples for even more though (fruit is more of a present or luxury than an everyday food in Japan). Some dollar stores did oddly carry fruit though, but I didn't really trust dollar store fruit.
Japan has food scarcity. A lot of their food is imported, and they lost a big chunk of farmable land after the 2011 Tohoku Earthquake. Most of the water near and around Japan is extremely contaminated as well, affecting the food. Whoever made the statement about Japan being a first world country and assumed the food is okay there is dead wrong. Even the food safety and handling there scares me.
Japan really made me appreciate all the land, safety, and good people we have in America.