The order of the sites you will visit may depend on
for which night you can reserve accommodation especially in Koyasan, Miyajima Island and Takayama,
and for which day you can reserve admission to Ghibli Museum, Mitaka.
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http://www.lawson.co.jp/ghibli/museum/ticket/english.html[Hiroshima, Miyajima, Takayama and Shirakawa-go]
It sounds nice if you can reserve accommodation
for the two or one night from 7 or 8 April in Miyajima Island
and for the night from 9 April in Takayama.
: You can use a 7-day Japan Rail Pass from 7 through 13 April, making it cover rail fees for your way back to Narita Airport [NRT].
: At Hiroshima Port, the tide will become low at 48 cm at 14:36, 8 April 2013 and high at 331 cm at 9:01, 9 April 2013. The timings may differ a bit at Miyajima Port, but if weather permits, you can catch two scenes of Itsukushima Shrine with a large gap in tides.
: You can make a daytrip from Takayama to Shirakawa-go.
: If time permits, you might consider staying for one more night in Takayama.
Between Miyajimaguchi Station and Miyajimaguchi Peer of JR West Miyajima Ferry you probably will need to go through an undergrounds pathway. Feel free to ask a station attendant how to get to the peer. The ferry fares are covered by a Japan Rail Pass.
It requires about 6 hours or more to get from Miyajima Island to Takayama City.
According to current timetables, if you leave Miyajima Island after 9:00, the next rail connection begins after 11:00 at Miyajimaguchi and ends at 17:08 at Takayama.
With a Japan Rail Pass you cannot take NOZOMI or MIZUHO trains, so you probably will need to change Shinkansen trains until reaching Nagoya.
[Narita Airport, Tokyo and Kamakura]
1:Narita - Tokyo - overnight bus to Kyoto When will your plane arrive?
I suppose you had better take a rest after a long chain of flights.... Consider staying for the night in Tokyo, near the departing place of the bus.
A one-way Suica & N'EX package can be a good choice.
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http://www.jreast.co.jp/e/suica-nex/index.htmlRail diagrams may get revised in March, so check the newest timetables.
At a JR-East counter in NRT you can turn in your Exchange Order for Japan Rail Pass, check timetables, get your Suica & N'EX package and try reserving seats
of Narita Express (which requires reservation) for Narita Airport / Airport Terminal 2 -- Tokyo / Shinjuku, Shinjuku / Shinagawa / Tokyo -- Airport Terminal 2 / Narita Airport,
of Shinkansen for Shin-Osaka -- Hiroshima, Hiroshima -- Nagoya, Nagoya -- Shinagawa / Tokyo,
and of Ltd. Express (WideView) Hida for Nagoya -- Takayama, Takayama -- Nagoya.
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http://www.jreast.co.jp/e/customer_support/service_center.htmlIf you visit Kamakura and Ghibli Museum, Mitaka after coming back to Tokyo, Shinagawa area sounds nice to stay in.
From Shinagawa Station it requires less than 1 hour to get to Kamakura Station or Mitaka Station, and you can take a direct Narita Express train to get to NRT.
[Kyoto, Koyasan, Nara and Osaka]
If you take a non-JR highway bus to Kyoto, the bus will probably arrive close to Hachijo Gates, not close to Central Gate [Karasuma Gate] of Kyoto Station.
Nankai does not have a station in Kyoto City.
You can purchase a Nankai Koyasan World Heritage Ticket
at a KNT branch on the Hachijo side (open from 10:00)
or at a JTB branch on the Karasuma side (open from 10:00 or 10:30).
I recommend you would stay in Shin-Osaka area or another area along subway Midosuji Line before heading to Hiroshima.
Shin-Osaka Station is the only Shinkansen station in Osaka City.
Kyoto - Nara You will make a daytrip to Nara, right?
Kyoto: Track 8, 9 or 10 {Miyakoji Rapid, in 45 min. or so} Nara.
: The one-way rail fare is 690 yen.
JR Nara Eki: Pole No. 1 {Bus Line 70, in 9 min. or so} Todaiji Daibutsuden.
: The bus fare is 200 yen per ride.
: From the 10th to 16th hours, the Line 70 buses depart twice an hour from JR Nara Eki.
Todaiji Daibutsuden {Bus Line 70, in 3 min. or so} Kasuga Taisha Honden.
Kasuga Taisha Honden {Bus Line 70, in 11 min. or so} JR Nara Eki.
: The last bus departs at 17:21.
Nara: Track 3 {Miyakoji Rapid, in 45 min. or so} Kyoto.
: Trains running for others also use Track 3.
Kyoto: Track 4 or 5 {Special Rapid, in 30 min. or so} Osaka.
: The one-way rail fare is 890 yen to Shin-Imamiya.
Osaka: Track 1 {Yamatoji Rapid, in 15 min. or so} Shin-Imamiya: West Gate.
: Trains running for others also use Track 1.
Nankai trains and cable cars are available between Shin-Imamiya and Koyasan.
The route to Osaka depends on the location of your accommodation.
Enjoy your trips!