Transportation within Japan

Hi!! I am planning to visit the below places as a couple.

Day 1 arrive Tokyo (7.30 Am Narita) head straight to Fuji Five Lakes
Day 3 Fuji Five Lakes (Early morning) to Kamikochi - Takayama
Day 4 to Day 6 Takayama - Shirakawago - Kanazawa
Day 7 to Day 10 (4 days) Kyoto
Day 11 to Day 12 (3 days)Osaka
Day 13 to Day 15 (3 days)Tokyo

Questions:

1. How do I reach Narita to Kawaguchiko?
2. How do I reach Kawaguchiko to Kamikochi? Current option Take the Fujikyuko bus to Takayam at 8.11 and get down at Hirayu Onsen. Is there a faster way or simpler way to reach there earlier than this?
3. Planning to take the Takayama Hokuriku Area Tourist pass for journey from Takayama to Kyoto. Any other suggestion?
4. What is the best pass to use for travel within Kyoto and Osaka?
5. How do i reach Osaka to Tokyo? Preferring an overnight bus.

How do I reach Narita to Kawaguchiko?

Looks like you have ample time to catch NARITA EXPRESS 8:

NARITA AIRPORT TERMINAL1 09:15 KAWAGUCHIKO 12:43
NARITA AIRPORT TERMINAL2 09:19 KAWAGUCHIKO 12:43

. What is the best pass to use for travel within Kyoto and Osaka?

Just single ticket, some JR trains take 30 mins, \ 560.

1. Has been answered. You can use Hyperdia (hyperdia.com/en) or Google Maps to find public transport routes.

2. No experience.

3. Make sure the pass pays off. You can buy single tickets if it is not cost-effective. Hyperdia can give you train fares.

4. An IC card (reloadable public transport card). Can be used in other areas too (but not all). There's a page about them on this website.

5. You've already said you want an overnight bus. Google it for info on companies (or look it up on this website). Other than that you can take a shinkansen (more expensive) or fly (not usually recommended).

[Re: Question 1]

Looks like you have ample time to catch NARITA EXPRESS 8:
Has been answered.

No; Narita Express trains do not daily run to Kawaguchiko Station.
(Using a route-finding tool without setting a correct date may lead to a wrong conclusion.)

When will you travel?

[Re: Question 3]

That pass does not pay off in traveling Takayama -- Shirakawa-go -- Kanazawa -- Kyoto or Osaka.

13500 yen: Takayama-Hokuriku Area Tourist Pass.

11770 to 12170 yen
: 2470 yen: Takayama -- Shirakawa-go by bus,
�@1850 yen: Shirakawa-go -- Kanazawa by bus (#).
�@http://www.japan-guide.com/bus/shirakawago.html
: 7450 to 7850 yen:
�@Kanazawa -- Osaka by rail, for about 2 and a half hours,
�@on a Limited Express Thunderbird with seat reservation.

Kanazawa and Osaka are connected by bus (#), through there are only two shuttles a day.
The one-way fare until Kyoto is 4400 yen.
Please note that the bus stop in Kyoto City is not near Kyoto Station.
: Kenrokuen-shita 07:10 -- Kanzaawa Station East Entrance (Bus Stop No. 2) 07:25
�@-- 11:04 Kyoto Fukakusa -- 11:59 Osaka.
: Kenrokuen-shita 16:30 -- Kanazawa Station East Entrance (Bus Stop No. 2) 16:45
�@-- 20:24 Kyoto Fukakusa -- 21:19 Osaka.

# : On this bus section, reservation is mandatory.

[Re: Question 4]

An IC transportation card is not a pass which allows you to have unlimited rides.
It basically does not give you a discount.

To visit major tourist spots in Kyoto City,
a Kyoto City Bus & Kyoto Bus One-Day Pass may be useful,
which pays off when you have three or more bus rides in the usage area.
http://www2.city.kyoto.lg.jp/koho/eng/access/transport.html#cvcrd

What sites in Osaka City do you plan to visit?

For: Kawaguchiko to Kamikochi

Take a train from Kawaguchiko to Otsuki.
This is usually the Fujikyu private rail, but there are a few JR trains that use these tracks. By the way, if you have a JR Pass, you may have to pay a surcharge.

Otsuki is on the Chuo line, that runs from Shinjuku to Matsumoto. Take either JR Chuo liners, or, the JR Asusa Limited Express train to Matsumoto.

Matsumoto has a nice castle to visit:
http://www.japan-guide.com/e/e6051.html

Finally, here is the "how to get there" page for Matsumoto to Kamikochi:

http://www.japan-guide.com/e/e6040.html#/section_getThere

I hope this helps.

Looks like you have ample time to catch NARITA EXPRESS 8

This direct train to Kawaguchiko only runs every Sat and Sun. Any other day, with NEX, you must change train at Shinjuku and Otsuki.

Looks like you have ample time to catch NARITA EXPRESS 8

This direct train to Kawaguchiko only runs every Sat and Sun. Any other day, with NEX, you must change train at Shinjuku and Otsuki.

How do I reach Kawaguchiko to Kamikochi? Current option Take the Fujikyuko bus to Takayama at 8.11 and get down at Hirayu Onsen.

The Fujikyuko bus would be a better option. With only one transfer you would arrive at Kamikochi before 13:00. However, you would not have much time to soak up the beauty of the area if you have to leave soon for Takayama.
Kamikochi is worth at least an overnight stay, especially if you are a nature enthusiast.
http://www.japan-guide.com/e/e6040.html

Thanks all. What time is the last bus from Kamikochi to Hirayu Onsen/Takayama?

How many hours do I require to cover Kamikochi?

As per current plan, I reach by 1 pm my plan was to spend about 5 hours there.

The alternative option is to reach Takayama from Mt.Fuji and come back to Kamikochi the next day. But that would be on 15th November. I m told the route closes on 15th Nov. So is it advisable?

Thanks for the detailed response Omtonishi. I arrive on the 12th Nov which is a Sat. So I guess we should have the Narita express.

I have not got my Osaka itinerary. What would you recommend for 2 days in Osaka? I am planning to do a trip to Mt. Koya from Osaka.Would you recommend Nara?

I arrive on the 12th Nov which is a Sat.
So I guess we should have the Narita express.

It seems you won't.

JR-Fujikyuko through N'EX trains will be available until 25 September 2016 on Saturdays, Sundays and public holidays.
Such through operation may be scheduled again during another season,
but currently there seems to be no official announcement made by Fujikyuko about that.

Please note that if the destination of your Narita Express is Yokohama or Ofuna, it does not run via Shinjuku.
In that case,
you can make a transfer in Tokyo Station, though it's a long way to go,
from the Sobu Underground Platform on the 5th basement
to the platform for Tracks 1 and 2 above the ground,
then catch a Special Rapid or Rapid train for Shinjuku.

A Narita Express train leaving NRT which has two destinations is separated in Tokyo Station into two trains,
one is to run for Shinjuku and the other is not.

Currently there is no railroad station in NRT Terminal 3.
If you arrive to NRT Terminal 3 and hope to take a train, you should go to Terminal 2.

- JR East Travel Service Center
http://www.jreast.co.jp/e/customer_support/service_center.html
: Here you can try to reserve your seat in a Narita Express train.

What time is the last bus from Kamikochi to Hirayu Onsen/Takayama?

You will take two buses to Takayama.
The last connection on 14 November 2016
: Kamikochi (17:00) -- (17:25) Hirayu Onsen (17:30) -- (18:31) Takayama.

I recommend you would try to catch at Kamikochi the second last 16:30 bus at latest
so that you won't have to worry about your transfer time at Hirayu Onsen.

How many hours do I require to cover Kamikochi?

Well, that may depend on persons;
in the japan-guide com article,
it is explained that hiking the trails along Azusa River from Taisho Pond to Myojin Bridge takes only a few hours.
http://www.japan-guide.com/e/e6040.html

Day 11 to Day 12 (3 days)Osaka

Here "3 days" seems to be a typo for 2 days.

What would you recommend for 2 days in Osaka?

You have various options.
How are your interests and preferences?