Tokyo Disneyland and DisneySea provide wheat free menu but only available in some restaurants. You can check which restaurants and the menu at Tokyo Disney websites.
Here's the link to both parks, in English, with a list of restaurants that will provide wheat free food and when you click on the restaurants themselves it will show a picture of what it is and what it does/does not contain.
I too have a glutton allergy. We've found that no matter which restaurant we go to at Tokyo Disney Sea or Land, that telling the server about your allergy usually gets you a visit from the manager, who will discuss the menu with you and make sure you find something good.
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