Whole wheat bread can be found in Japan--only you have to look hard. These bakeries do not advertise in English. If you're willing to buy on the Web and have a Japanese friend to help with ordering, you can purchase from here:
直达号
There are a number of organic bread bakeries around Tokyo and Yokohama, as well as in other parts of Japan. Many are small in scale and do not advertise, since they cater only to the neighborhood where they are located. You'll need to talk to Japanese friends who are knowledgeable in organic foods to find a bakery near you.
As for pizza, Japan has Domino's, Pizza Hut and other delivery pizzas, as well as pizzerias that serve Italian-style pizzas.
There are also teriyaki burgers. The one that serves very good teriyaki burgers is a Hawaii hamburger chain called Kua'aina.
HTH!