All the places you noted under Kanto:(Shibuya,Harajuku, Akihabara,Roppongi, Ikebukuro,Tokyo tower,Ginza, Shinjuku, Imperial Palace /Gardens) are within the JR Yamanote loop line (Google it and enlarge the map). Most of these are really similar: Shinjuku, Shibuya, Ikebukuro, Ginza,Roppongi (google them al). They are basically shopping area with really big departments stores, thousands of small stores, restaurants, office buildings etc. you can pickup and chose only a few then visit different and more interesting places outside Tokyo like Kamakura or Nikko (1 day each). In Tokyo I would definitely see Shibuya, Harajuku (including the Meiji shrine) the Imperial palace gardens (you can't visit the Palace, unless by special appointment, and it is a bland thing)and Ginza --10 minutes walk from the Palace area--. This will take one day at a leisure pace. Another day I would see Asakusa--the funky old Tokyo-- then Akihabara (stores open around 10)then the Tokyo tower (not the most exciting place) and Odaiba. You can add Roppongi (not the most exciting place for me) the day you see the Ghibli museum. in the Kansai: Osaka kita and minami are about 30 minute apart (by walking)see kita in the morning =early afternoon and minami in mid-afternoon and evening (especially the Dotonbori area). this will be a full day. You may be able to squeeze in the castle. In Kyoto: Kiomizu dera, the philosopher walk,the Heian shrine, the Pontocho and Gion areas (late afternoon) will take one day at leisure. Another day you could see the Fushimi Inari shrine in the morning and the Arashiyama area in the afternoon. Another day you must go to Nara. You should also go to Himeji castle one morning and stop in Kobe (Kitano area, Sannomiya, then Mosaic by the port) in the afternoon. In both Tokyo and Osaka do check the arcades (shopping streets for pedestrians only, with a roof) This is a short list..You could stay in one place only: Osaka or Kyoto as they are close to one another and your pass let you travel freely. As others have noted only buy a 7 days JR pass for the visit to the Kansai. Going to Kamakura isn't expensive at all. if you really insist on seeing all the Tokyo areas on your list that I didn't talk about you can do it in one afternoon by doing a round trip by the Yamanote and getting on/off. But, again,I would miss Ikebukuro, Shibuya, etc. and instead check Ueno, Yanaka, Shinagawa.Check this site(under Japan A-Z: Transportation/railways/ passes etc.) for day passes etc. DON'T FORGET to check Yodobashi cameras (Tokyo or Osaka) for an incredible choice of cameras, TVs etc. plus the most amazing refrigerators and washing machines (no kidding) you are likely to see plus microwave ovens that bake, broil, steam, and all sorts of things...
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