[Hatix]

Well, how far is Harajuku from Tokyo..., erm, Harajuku is a neighbourhood IN Tokyo. Remember Tokyo is the biggest city in the world, it has 23 wards which contain a lot of neighbourhoods.
And Yokohama just blends into Tokyo, you could say it's one big city. Take a look on Google Maps and see for yourself. Also, Tokyo has one of the biggest subway & train systems in the world, so depending on your hotel in Tokyo, you'll be in Harajuku in 10-40 minutes depending. But there's another (and a bit more choice) reseller shop in Ueno too. But you should find all these shops somewhere in this thread as well, with descriptions how to find them.

The Yokohama Arena layout, you can find on the site of yokohama arena. It will probably be the same as last time, so that means 3 blocks wide and 4 blocks long in the center. (go a few pages back in this thread and you should find quite a lot of discussion about this ).

And for some extra info: when you fly to Tokyo, you're actually flying to Narita, that is where Tokyo International Airport is, which is one hour by train from the city .
Try to read something about Tokyo on japan-guide.com too. You'll find a lot of interesting things to see and do in Tokyo there as well, and there's quite a lot. How long are you going to Japan? If you're going 2 weeks, I'd recommend 1 week Tokyo and 1 week more to the south (Kyoto, Osaka, Nara, Himeji).
(Btw: you can read about my previous trip(s) on my blog, link in signature ;p) Feel free to ask more info if you want