OK, here is my challenge.

I will eat just about anything so no problems there. However, my wife is much more particular, and unfortunately, her dislike/won't eat category coincides badly with the Japanese diet.

1. No shellfish.
2. No raw fish.
3. Absolutely no oranges.
4. Not a fan of tofu.
4. A myriad of other specific items to be avoided.

I don't worry that it will be possible for her to eat in Japan, but at the same time, I don't want to miss all the things that I really like -- Shellfish and Sushi/sashimi. Also, many of the restaurants that I have seen offer course menus where you don't really know what you are going to get til it's brought to you or includes one or more courses on the list above.

Kaiseki seems to be out.

Can you order tempura courses without shrimp? or by the piece?

Any suggestions for eating choices? Are restaurants willing to make changes substitutions to their menus?