This review is current to 14 Oct 2013 as I went there today. I went there to hunt a variety of kit kats but was amazed at what else was there. It was very busy with queues for ramen shops, delicious looking ice creams and there were many themed shops, e.g. Hello Kitty, Miffy, Lego, Gandam etc.
However, I finally found the Kit Kats at the Shokoku Gotochi Plaza store. It is located now right at the end of the Tokyo Ramen Street on the South Side of the basement. Unfortunately, the website only has a Japanese map so I tried to take a photo of the English map/pamphlet. If you refer to this picture, in the bottom left you can see an arrow that says Tokyo Ramen Street. It is pointing to an orange store with a number one. Just to the left of this you see a pink box/store with the #1 - this is the Shokoku Gotochi Plaza store with Kit Kats and other goodies. There are 2 ends of the basement. I initially found myself at the Lego store which is on the extreme north end so just go the other way and if you start seeing ramen restaurants you know you are heading the right direction.
Kit Kat Flavours included (refer to picture of Kit Kats which were at front of store):
Wasabi
Purple Sweet Potato
Sweet Red Bean Cream Sandwich
Cayenne Pepper Powder
Rum & Raisin,
Apple
Strawberry Cheesecake
Citrus Golden Blend
Hot Japanese Chilli
I understand that varieties may change with season and most were c.¥840.
For the green tea or strawberry varieties fome of the Donki/Don Quijote stores have them for c. ¥300. Otherwise you can purchase them at the airport. There are 2 x green tea varieties - sweet and normal from my understanding.