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?

Maybe you could get a recommendation from your hotel for a robatayaki (Japanese barbeque) place that offered the usual grilled chicken for your wife, but had sashimi (somewhat unusual, but not unheard of) for you. More likely you'd get your fish grilled, though.

Also, depending on your interest, you may want to look for "What's What in Japanese Restaurants," by Robb Satterwhite, ISBN 4770020864

Why don't you try an Izakaya? It's like a place where you can drink and eat. All of the ones that I usually go to will have an wide mix of Japanese cuisine e.g. I could be eating slices of raw horse meat while my kids get kabocha (squash) tempuras.

Your hotel could recommend one nearby.

In Japan many restaurants actually have plastic replicas of what you get displayed in the window so you can see what is included and how the food will look.

Bring Frosted Flakes.

Teppanyaki
Shabu Shabu
McDonalds
Mister Donut
KFC

Plenty of available items.
Yes tempera can be made without prawns.
There's also Ramen, Udon and a myramid of noodles available to try.
No raw fish, there's cooked fish. Steak, shabu shabu, etc etc along with the items already mentioned.

Have her food restrictions written down in Japanese, preferably before your trip or latest at your first hotel in Japan. It's easy to slip the note to the chef and ask him/her for "omakase" keeping the dislikes in mind.

Many tempura specialty restaurants have a vegetables-only option or can be persuaded to fix one up for you. There's also a variety that has cooked regular fish instead of prawns.

Almost everyone likes yakitori, especially the kind with alternating bits of chicken and green onions.

Izakaya and robatayaki places are a good suggestions, in that they specialize in preparing what our restaurant industry calls "small plates."

This is very much in the fast food catagory, but in Hong Kong and Manila I enjoyed a chain restaurant, Yoshinoya I think was the name, that served a beef bowl, basically a bowl of rice with strips of beef on top and broth poured over it.

Quite tasty, but - as I said - fast food dining.

This is a good idea. Also, a number of places will bring you a bento with some of the side dishes that your wife won't eat. You can eat those while she eats the rest. Just make sure beforehand that the main dish is something she will eat, like cooked fish.

If you are a big fan of sushi/sashimi, do not even think of taking her to a good sushi place. There will be nothing for her to eat, except cooked eggs and cucumber rolls. In some places the chef will be personally insulted if you reject his food, and you may want to avoid that.

A lot of places (for example, izakayas and regular restaurants) will also offer sashimi in addition to other things, but that's not the prime stuff. Edible to very good, but rarely for the connoisseur, except at high-end kaseiki or kappo places, which you rightly point out should avoid. At those high-end places substitutions could be considered an insult, since the order, arrangement, and choice of food follows a particular pattern that somebody spent hours fretting over, and you do not want to upset the wa that way. The unscripted agreement is that you will be taken care of, and you are to be grateful for the care you are being given. Making ripples in the water is not appreciated.

If you are big sushi fan, you may want to have the talk with your wife. This is the talk my mother and father had. My mom doesn't really go for raw fish and shellfish, while my dad just loves it, it is probably his favorite food. So the talk was one where my dad told my mom that one night during their trip my mom would have to find herself a place to eat, because he was eating sushi, come hell or high water. They horse traded something, don't remember, but it was along the lines of "then tomorrow we go to the Ginza to look at kimono silks to make a dress for your daughter's wedding" or something like that.

The downside of this is that you may not want to eat sushi anywhere else after that.

There are some excellent French and Italian restaurants in Japan. Many of them will be using the same fresh ingredients as their Japanese counterparts and it's easier to order around your wife's dislikes.

Any department store, go to the food floor. You will see an replica of what is on the menu. Your wife can choose what she wants. The food is pretty good.

If your wife loves shopping, then this plan is a BAD idea. You will never get to eat.

For the last few years, Yoshinoya as a chain has been suffering badly because it couldn't offer beef due to the Japanese boycott on imported beef. That may still be in place.

RichardInSF it was USA Beef that did them in.......they have since started again(with one day sales etc.) but ramping up the imports and gaining the Japanese consumers trust will be a long road. BTW, Aussie Beef just doesn't cut it at those restaurants as it is too lean(IMO).