First post but just thought I'd add some recommendations as I lived in Japan for a few years on the island of Shikoku.
Tokyo - my favourite area is around Ginza as you get that cosmopolitan sophistication married with Asian energy that the city is famous for. If you are a vinyl lover, Tokyo will be paradise as there are record stores aplenty but it will take weeks to trawl through them all - hotspots are in Shinjuku and Shibuya. If you want to see street fashion and cosplayers try Harajuku. I'm sure your guide will take the group to Sensoji temple in Asakusa as that is one of the must-dos in Tokyo.
Takayama - my favourite spot! The markets are good. Beautiful spring colour in the mountains. Make sure you try some of the onsen here, too. Hopefully you will have a side trip to Shirakawago for the historical thatched buildings.
Hiroshima - Peace Park and Museum. Eat some Hiroshima-style okonomiyaki (savory cabbage pancakes with noodles and meat of your choice). Side trip to Miyajima which has the famous "floating" torii shrine gate.
Kyoto - Amir likes the Golden Pavilion but I prefer the silver one for its gardens. Walk from there along the Philosopher's Walk to Nanzenji for the cherry blossoms (sakura). Gion district is good for spotting geisha or maiko (and lots of Chinese or Korean tourists dressed up like maiko). Kiyomizu-dera for views and the sacred water. Arashiyama for bamboo forests and spring colour. If you are in Kyoto during sakura season you will have millions of other sight-seers to jostle with.
Your guide will be indispensable in all the hustle and bustle of the cities. There are electronic superstores dotted throughout the big cities that are good for browsing on rainy days -- try Yodobashi Camera. Biccamera, Yamada Denki.
If you don't want to eat seafood, there are other options such as okonomiyaki, ramen, donburi, yakitori/yakiniku and izakaya food (as mentioned). There are also plenty of western-style cafes around every corner. But you might be surprised by how good the seafood experience is in Japan. I normally won't eat sashimi (raw fish) in other countries but every time I visit Japan I am amazed at how good it tastes there.
If you are there during sakura season, you must, must try hanami: picnicking with a group of Japanese people under the blossoms, drinking sake, singing songs, composing haiku, whatever! This is considered one of the quintessential Japanese pastimes.
Enjoy!
Richard
