Day 1 - Arrive Narita Airport, pick up Suica / N'ex pack, swap exchange order purchased in advance for the JR Rail Pass, take train to Tokyo, check into hotel (Shinjuku), Takashimaya Department Store across the street from Shinjuku Station's south exit, Tokyo Metro Building Observation Deck, also near Shinjuku Station, sleeeeeep.
Don't the seats on the trains look awesome?

That's the Keisei Skyliner, we will actually be on a different train, but it also has some pretty nice looking seats.
Day 2 - Late start, Nakano for shopping in the Sun Mall and the arcade leading up to it, includes Mandrake, a shop specializing in all things manga, dolls, and cosplay (Hide your wallets! hehe) Evening Shinjuku area after a stop by Tokyo Tower for Cando, Natural Plenty, Shop 99 after dinner.
Day 3 - Harajuku - Meiji Jingu Shrine, Takeshita Dori (Harajuku Daiso, Chocomilk, Kiddy Land, Oriental Bazaar, and other shops and restos), Ukiyo-e Ota Memorial Museum for woodblock prints, Omotesando, and walking on over to Shibuya for the crazy intersection in the evening. Maybe hunt down CouCou near Daikanyama Station if it isn't too late for their 8 pm closing.
Harajuku Station

Shibuya Intersection
Day 4 -Tsukiji Market early am, breakfast jogai-shijo (outer market), 9am entry inner market walk thru, Hamarikyu Gardens park for water bus (Sumida River Cruise) to Asakusa (about 45 min), Sensoji Temple (Asakusa Kannon) for lunch, shop, see temple, retro Hanayashiki Amusement Park (thanks Ilbonito!), maybe Edo Shitamachi Traditional Craft Museum, Kappabashi Dori, dinner in the area, sleeeeeeeeeeeeeeeeep!
A picture of Tsukiji (pronounced tSKIgee).

Day 5 - Asakura Choso-kan Garden, subway to Nezu Station For Nezu-jinja Shrine, subway to Ueno Station for Ueno Park Kyu-Iwasaki-tei Garden 11 am tour, catch the 1:30 Green Tour if possible, rest of day in Ueno Park area. Shitamachi Fuzoku Shiryo-kan, Shinobazuno-ike Pond (swan paddle boats - don't ride with your beloved as legend says you will break up within one year, thanks to the jealous goddess Benzaiten enshrined in the temple!), Uneo Toshugu Shrine, Tokyo National Museum, Tokyo Western Museum, and the Ueno market, Ameyoko Market Street, be sure to look for the traditional medicine shop with all the snakes in the window,(leave from by the zoo).
I think the Toshugu Shrine looks awfully cute.

Thanks to Japan Guide for the picture.
Day 6 - Start Rail Pass here with early start to Kurihama for the Tokyo Wan Ferry across Tokyo Harbor to Chiba, then the ropeway up Mt Nokogiri to see the Nihon-Ji Daibutsu, the tallest carved stone Buddha in Japan. Take a bento lunch to the park and enjoy most of the day here. Be sure not to miss last cable car down the ropeway as it is about a 3 hour walk to arrive back at the station. Return in time to turn teen loose Higashi-Ikebukero for squealing girl shopping while we check out the posh Times Spa Resta for a super sento onsen experience.
Photo of the giant Buddha.

Day 7 - Sanrio Puroland opens 10am Tama City, stay until around 1:30, back to the station and train to Ghibli Museum, stay until closing at 7 pm and back to Tokyo for bed.
I hope dying your hair purple is optional. *teehee*
Day 8 - Edo Wonderland for a cool trip to Edo-period Japan. They even let you dress up in costumes, walk on stilts, and do other cool edo period things.
Day 9 - Akihabara for Game Taito Station, Comictoranoana, Animate, and lunch, then train from Akihabara to Kami-nakazato Station for Northern Tokyo Disaster Research Center for EARTHQUAKE!! Zomg! Take a bento snack on the Hikari Shinkansen to Kyoto, check into hotel and early bed.
Photo of Game Taito Station, Comictoranoana, and Animate courtesy of Richard Pluck - that's Animate on the left.

Day 10 - Hiroshima for the Miyajima Itsukushima Shrine and the Peace Memorial, shrine closes at six, 2 day passes are available at visitor center that include street cars, ferry, and ropeway for 2,000 yen.

See Adekun's blog where this picture came from for more great pictures and information!
Day 11 - Kiso Valley to see some of the preserved towns. Tusumago is a must see as it is best preserved and has banned car traffic from the main road.
Photo of the Kiso Valley courtesy of Japanese Wa-pedia. Who knew they had their own wiki?

Day 12 - Last day of Rail Card - Take first bus to Kozanji Temple (Toganoo-san)in Takao area to view the first recorded manga (actually a copy, the originals are in Tokyo and Kyoto National Museums). Train to far northern Kyoto forOhara for lunch at restaurant with foot bath while eating, then Otonashi no Taki waterfall, Sanzenin Temple, Shorinin Temple, Raigoin Temple, and shopping and restos on the path from town. May book ryokan with onsen for overnight.
Day 13 - 11 am Kyoto International Manga Museum, see if we can pry teen out for later lunch, Marumasu Nishimuraya Yuzen Kobo for kimono painting lesson on a t-shirt (90 min) near Nijo Castle, which we will see after. Try to squeeze in some shopping at Nishiki Market and Teramachi Street, then possibly walk along Pontocho to see if we see Meiko, and dinner.

Thanks to JapanVisitor for the picture, click for further information on Pontocho.
Nijo-jo
Day 14 - Take the train out to Arashiyama Station by 9 for Sagano Romantic Train out and Hozugawa Boat Cruise back, lunch in Arashiyama area. Kyoto Walking Tour Itinerary - Yasaka Shrine, Maruyama Park, Kodaiji Temple + Kodaiji Rakusho Tea Room, walk by Ryozen Kannon Temple upstairs - Sannenzaka, Jishu Shrine w couple rocks, Kiyomizu[/url Temple and Taki-no-ya snack pavilion, [url=http://www.flickr.com/photos/grumpywolf/3035780665/ new=true]Otani Mausoleum, Toribeyama Graveyard, Kawai Kanjiro Memorial House, Kyoto National Museum, Sanjusangendo Hall (says 5 hours).

From Babibuebo blog, see for more details and the most amazing pictures!
The Kiyomizudera temple, courtesy of Japan Guide.

Day 15 - Philospher's Path from Ginkakuji to Nanzenji, stopping at Eikando Temple, shopping, and snacking along the way. Daughter to be made up as a maiko and studio pictures, unless parents are allowed to stay we will head to Kyoto Craft Center or Kyoto Handicraft Center. Gion for late show and tea at Gion Corner.
Day 16 - Returning home from Osaka, if time permits a brief stroll at one of the gardens before leaving.
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