9 Day Itinerary Revised

Thank you to everyone who provided their input on my last post! I have taken most of your advice and applied it to this new itinerary….. The biggest changes are that instead of going to Fujinomiya we are going to Hakone for two nights, Hiroshima has been dropped completely for an additional day in Kyoto, and except for 4/1 each day is now dedicated to exploring a specific area instead of specific sights; for the most past…. Also travel will still be done by public transit but we will no longer have the rail pass….. Again even with this new itinerary I know this trip will feel rushed, but that is due to the time we where able to get off of work and unfortunately that is unchangeable….. Below is the new itinerary and below that are some of the things I had questions about or wanted advise on:

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3/28: Tokyo

* Land at Haneda roughly around 1600
* Head to our Hotel which has been moved from Akihabara to Shinjuku Hotel Rose Garden for 3 nights

3/29: Tokyo

* This day is completely dedicated to exploring the Shinjuku area and to recover from jet lag
* Ninja House
* Samurai Museum (if reopened)
* Hanazono Shrine
* National Garden

3/30: Tokyo

* In the morning: Ghibli Museum
* After: Akihabara Electric Town
* Late Evening: Ueno Park

3/31: Tokyo/Hakone

* Morning to late afternoon: Shibuya
* Meiji Jingu
* Cherry Blossom Garden
* Hachiko statue
* Arrive at Hotel Green Plaza Hakone (2 nights) around 1730

4/1: Hakone

* Owakudani
* Hakone Ropeway
* Hakone Open-Air Museum
* Enjoy the Onsen at the hotel

4/2: Hakone/Kyoto

* Leave around 0900 for Kyoto
* Downtown/Station area
* Manga Museum
* Nishiki Market
* Stay at Hotel Wing International Kyoto-Shijo Karasuma (4 nights)

4/3: Kyoto

* Fushimi
* Gekkeikan Okura Sake Museum

4/4: Kyoto

* Arashiyama
* Monkey Park
* Daikaku-ji Temple

4/5: Kyoto

* Morning: Imperial Palace
* Afternoon/Evening: Higashiyama
* Hokan-ji Temple
* Kiyomizu-dera Temple

4/6: Kyoto/Narita Airport

* Leave by 0700 for Narita Airport for 1830 flight

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Questions:

* Should I buy train tickets in advance?
* When buying train tickets do you buy your entire journey at once or do you have to buy your next ticket at your layover station (not sure on the terminology here)?
* Should I buy hotels in advance?
* Should the order of this trip be flipped so that Kyoto is first and Tokyo last?
* Additional landmarks to see at each place?
* Your favorite stores to visit especially in the Tokyo districts?
* Are the chosen hotels good or would you recommended staying elsewhere?

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Thank you in advance for your advice!