The staff was very knowledgable about gluten allergy. They have soy sauce only made from soy, can make gluten free ponzu sauce (rare to find in Japan) and assured me the food would be prepared separately. The waiter was very kind!!
Staff are well aware of Gluten Free and carry separate Gluten Free soy sauce. Not everything on the menu can be gluten free due to use of Miso but there is plenty to choose from.