Hiroshima is known for its Okonomyaki and there is a whole district dedicated to its preparation. It is also known for Anago, the salt water eels and you can find stalls everywhere on Myajima Island, which I am sure you have planned to visit.
In Kyoto, the Nishiki food market is definitely worth visiting and I was sent to a kai-ten place near Kyoto City hall called Moshashi, which is definitely one of the best I encountered on my trip.
If you have time, do what I did and spend a day with someone from the W.I.K, (Women's Institute of Kyoto) whose aim is to make connections around the world through a love of food.
I didn't warm to Harkone, but still remember the wonderful Gyoza at The Gyoza Centre of Gora, which are considered some of the best in Japan
In Tokyo, I had my best meals at the yaki-tori bars in the backstreets of Ueno, close to the station and became slightly addicted to the tori-karage (fried Chicken)
Also head to Ryogoku or "Sumo town" for the Chanko Nabe, the Sumo stew and make sure you spend time in the food halls of some of the larger department stores, if only to see square water melons and $100 bunches of grapes. Kappabashi is worth a trip to see the shops selling the plastic models of food that can be found outside just about any restaurant.
I am assuming you are visiting Tsukiji in Tokyo and that is definitely not to be missed. Get a guide and get there early. I thnk i was there about 5am and, with our guide had access to the auctions. Afterwards we ate at a place called Kujiro's
here are some posts from my EAT MY GLOBE blog
TokyoKyotoHiroshima and Tokyo Fish MarketHope any of this helps
Slapsie