There's an area in Shinjuku, Tokyo called Golden Gai. It's one block of tiny bars that sit 3-10 people max crammed together. Some places are exclusively Japanese but a couple of foreigner friendly ones we found were really awesome. Can't give you exact locations but if you walk around Golden Gai you'll see the signs. Check out:
- Turan bar - on 2nd floor, cheap cover charge with really good atmosphere and plays rock music
- Albatross - bit of a goth-y feel with all the velvet and chandeliers
- Deathmatch - must go if you like death metal and horror films
Bar Zoetrope in Shinjuku is a great whisky bar. You can Google for directions (it's on the 3rd floor I think). Bartender kind of speaks English so you can make a reservation over the phone if you wanted.
Akihabara is better visited on a Sunday when the entire main street is pedestrianised.
Tokyo tip, if you're staying just in Tokyo, don't get the JR pass. That's really only worth it for long distance travel. There's a Narita Express that goes directly from the airport which was good. The green car (first class) seats had massive leg room. To get around Tokyo, you can just get a Suica card from any train station. It works exactly like an oyster card in London so made dealing with the trains and tubes really easy.
Off Hiroshima you can visit an island full of just rabbits. Ōkunoshima is historically a poison gas factory, now it's overrun with rabbits that you can feed and pet to your heart's content.
Finally, I would definitely recommend renting a pocket wifi. http://www.globaladvancedcomm.com/pocketwifi.html
It made navigating around so much easier. There's not a lot of free wi fi and we found 3g quite expensive. They can post the wifi device to your hotel or you can pick it up from the airport. They then include a stamped envelope so you can post it back before you fly out. Simple.