Quick Tip: While in Japan, you can always find gluten free food at 7-11 or Cococurry. 7-11 can be found nearly everywhere in Japan, it doesn't matter how small the town is. Onigiri make a great gluten free snack or light meal, just be careful which one you pick. Consider this as a meal even if you don't have allergies as they are delicious and easy to pack.
Coco curry can also be found in any large city in Japan and offers a Japanese curry that is suitable for most allergies (apples are the main allergen). Just ask your waiter or waitress as it is not always on the menu. They are made off-site and heated in plastic bags so you can rest assured there are no contaminants that might make you sick.
If you need a break from sushi, consider these other options!