Day A:
Half Day Tour
Eat lunch in Shinjuku
Then head to Tokyo National Museum (Ueno Park)
Explore Akihabara (techie neighborhood) buy cheap electronics
Visit Edo-Tokyo Museum (Ryogoku Station)
Eat dinner in Ryogoku/Akihabara/Shinjuku

Day B:
Early Morning Sushi at Tsukiji Fish Market
Visit Tsukiji Honganji Temple
Walk through Ginza, find place to eat lunch
Then Imperial Palace (reservations made online)
Eat lunch
Head back to Sumina river boat to Asakusa (tentative)
Ueno
Toshogu Shrine (in Ueno Park)
Visit Sensoji Temple
Eat dinner

Day C:
Book a day tour to Mt. Fuji – Would be full day adventure and need to return by bullet train most likely

Day D:
Start the day off at Ota Memorial Museum of Art (near Harajuku)
Then head to Harajuku
Stop off at Yoyogi Park
Visit Meiji Jingu Shrine (in Yoyogi Park)
Eat lunch near Harajuku
Explore Harajuku and Shibuya (do majority of shopping)
Make sure to check out Shibuya crossing (as seen in Lost in Translation)
Eat dinner in Roppongi
Hit up Roppongi at night to check out the Ex-Pat community

Day E (1/2 day):
Explore Shinjuku
Go to Shinjuku park
Visit Tokyo Metropolitan Gov’t Building (deck on 45th floor, cafeteria on 23rd)
Day F:
Head to Nikko for a day trip
Other if time alots and there is money to spend:
Fire Walking: Happens in Mid-March at the foot of Mount Takao
Kabuki Performance