Coeliac is not as well understood here as it is in some other parts of the world, but there are gluten-free foods available. Rice, rice flour and rice noodles will be your friends.
For soy sauces, you’ll need to get a gluten-free version, as most of them contain wheat products. You can find these at health stores and speciality food stores. Most sauces in Japan contain wheat or some kind of gluten-y thing.
Soba noodles are gluten-free if they are 100% buckwheat, but many are blends, so you’ll need to be careful with those. Steer clear of udon noodles.
Those are just a couple of tips off the top of my head. You might find our healthy living guide helpful: https://tokyocheapo.com/food-and-drink/healthy-eating-tokyo/#tabo6
I’m not celiac, but I did manage to be almost 100% gluten-free in Tokyo for about 18 months.