Umm...I try to rearrange. Shrines, Temples and Gardens are closed by evening.The shopping quarters are O.K. So I think you can visit, if you group together.
Tue 17 - Fly in, arrive at 7pm. Stay in hotel near Tsukuji.(you can glance at Ginza)
Wed 18th - Tsukuji for breakfast, Ginza, Otemachi, Imperial Palace, Tokyo Station. Head to Kusatsu.
Thur 19th, Fri 20th - Kusatsu.
Sat 21st - Leave Kustatsu for Tokyo. Meiji Shrine(the sacred place), Harajuku, Shibuya(Hachi-ko statue and crossing).
Sun 22nd - Yanaka(What a tasteful choise!), Ueno(you can watch SkyTree), Akihabara.
Mon 23rd - Mt.Takao-san, Shinjuku, Metropolitan Government Office building.
Wed 25th - Imperial Palace Gardens, Yasukuni Shrine, Koishikawa Korakuen, Tokyo Dome City.
Fri 27th - Ghibli Museum, Edo Open Air Museum, Kichijoji.(so hard?)
Sat 28th - Asakusa, Senso-ji temple, SkyTree for view, Sumidagawa Fireworks Festival! (too crowded! secure your seat?)
Sun 29th - Hama Rikyu, Kyu Shiba Rikyu, Zojo-ji Temple, Tokyo Tower, Odaiba. Sengaku-ji Temple is interesting too.
Mon 30th - Nature Reserve(where?), Nogi Shrine, Roppongi Hills. Sanno-Hie Shrine is interesting.
Tue 31st - more Akihabara.
Thurs 26th - Day trip to Nikko.
Tue 24th - Day trip to Kamakura. Wed 1st - Day trip to Yokohama, Sankei-en garden, China Town.
Kawagoe is so far, Ikebukuro and Tsukishima are what you want?
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