Rail Pass- Kyoto-Takayama-Karuizawa-Tokyo

Hi All,
We have booked our trip as follow and need advice for the travelling part by train or bus.
13/12- Arr Osaka, travel direct to Kyoto (3N)by train.
Will do a day trip to Osaka by train.
16/12- Kyoto-Takayama (Nagano) 2N by train (start using 7 day pass) or Nohi Bus?
Will do a day trip to Shirakawa-go by Nohi Bus.
18/12- Takayama-Karuizawa (3N) by train.
Is 3N too many in Karuizawa or 2N will do? We plan to just relax and go slow, what can we do there?
21/12- Karuizawa-Tokyo (3N) by train.
Would like do day trip to Mt. Fuji, visible? Is 2 days enough to visit Fish market, Anime shops, Asakusa, Shinjuku, Harajuku. Or we do 2N in Karuizawa and 4N in Tokyo?
Should I get 7 days pass and start using on 16-21/12 (only 6 days), can I use the pass for day trip to Mt. Fuji for the 7th day?
24/12- Tokyo-Narita. Which is the cheapest way, bus or train?
Thanks in advance, cheers.
Lawrence

Takayama City is in Gifu Prefecture, not in Nagano Prefecture.
Karuizawa Town is in Nagano Prefecture.
It requires at least 5 hours, maybe more than 7 hours to travel by railroad from Takayama Station to Karuizawa Station.

If you make a Hakone trip (hoping to see Mount Fuji) mainly by non-JR transportations,
a 7-day Ordinary-Class Japan Rail Pass is likely either not pay off or not save much of your JR cost.
If you can fly into HND or NRT and fly out from KIX,
maybe you can save your railroad cost by using a JR Kanto Area Pass.

Where in Tokyo will you stay?
Which transportation mode(s) do you prefer? Are you OK to have a bus ride for more than 3 hours?

Hi Omotenashi,
Thanks for your suggestion.
We are arrive in Osaka and depart from Narita.
Bus ride more than 3 hrs is ok, I find it more scenic to travel that way. Can you help us plan our transport?
Not sure where stay in Tokyo, where would you recommend? A friend suggest Ueno as it's easier to go to Narita.
Cheers,

Hmm..., you are OK to have a long bus ride....
Then, possible routes are
: from Kyoto to Takayama by JR on Limited Express Hida 25 (#1)
(7450 yen per adult, departing at 08:31 and arriving at 12:15)
: from Takayama to Shirakawa-go and back by expressway bus
(4420 yen per adult for a pair of roundtrip tickets)
http://www.japan-guide.com/bus/shirakawago.html
: from Takayama to Shinjuku by expressway bus in the evening
(6690 yen per adult, about 5 and a half hours)
http://www.nouhibus.co.jp/english/tokyo.html
: from Shinjuku via Omiya to Karuizawa and back within 3 calendar days
(8300 yen per adult on a JR Kanto Area Pass)
#1: This train is the only Limited Express Hida train for Takayama which is available from Kyoto Station in a day.

You can travel from Kyoto City to Takayama City by expressway bus (at 4200 yen per adult), but according to the current timetables, Limited Express Hida 25 is scheduled to arrive to Kyoto earlier in a shorter time than the first expressway bus.

A JR Kanto Area Pass is a 3-day rail pass issued by JR-East.
http://www.jreast.co.jp/e/kantoareapass/index.html
If you start your Karuizawa trip from a JR-East station in Tokyo, this rail pass can cover JR train rides all the way (#2). Nagano Shinkansen section Tokyo -- Ueno -- Omiya -- Karuizawa is inside the usage area of this rail pass.
You can use this rail pass also between Karuizawa Station / a JR station in Tokyo and Odawara Station (#2) in a trip to and from Hakone, where you may have a chance to see Mount Fuji. (Odawara Station is between Hiratsuka Station and Atami Station, which are shown in the lower left of the area map.)
#2: One thing to note is that this rail pass cannot be used on Tokaido Shinkansen, which is operated by JR-Central.

The expressway bus line Takayama -- Shirakawa-go (-- Kanazawa) is co-operated by Nohi Bus and Hokuriku Railroad [Hokutetsu]. For some of the buses on this line, seat reservation is necessary.
The expressway bus line Takayama -- Shinjuku is co-operated by Nohi Bus and Keio Bus. Its east terminus is Shinjuku Expressway Bus Terminal. All the seats of all the buses on this line require reservation.
You can try reserving your bus seats on these two lines through a phone call to the reservation center of Nohi Bus.

A friend suggest Ueno as it's easier to go to Narita.

Keisei Skyliner trains are connecting Keisei-Ueno Station and Keisei stations in the two NRT terminals.
http://www.keisei.co.jp/keisei/tetudou/skyliner/us/ae_outline/index.ht...
Narita Express trains of JR-East are available between Shinjuku Station and JR stations in the two NRT terminals.
http://www.jreast.co.jp/e/nex/index.html

Currently there seems to be no discount ticket offered only for a NRT-bound ride on a Skyliner / Narita Express train.
For trains running to NRT, the second last station is Airport Terminal 2 Station, and the last station is Narita Airport Station (in Terminal 1).
Please note that Keisei-Narita Station and Narita Station of JR are located outside the airport.

Ueno is closer to Asakusa than Shinjuku is.
You can walk from/to Keisei-Ueno Station to/from subway Ueno Station (on Ginza and Hibiya Lines) of Tokyo Metro via an underground pathway (equipped with elevators).
You can get from/to the Ginza Line part of subway Ueno Station to/from Main Entrance of Ueno Station of JR via one escalator.
Ueno Station of JR is complicated, while the other two stations are rather simple.

Shinjuku is closer to Harajuku than Ueno is.
An area which may be called Shinjuku is wide, stretching over Shinjuku and Shibuya as municipalities. In your Shinjuku trip, a station where you get on and off trains is not always in Shinjuku Station complex.
Shinjuku Station complex is huge and complicated with many lines of several railroad operators.
Toei subway has Shinjuku and Shinjuku-nishiguchi Stations in the complex. Tokyo Metro has only Shinjuku Station there.

Let me add information regarding the above-mentioned expressway bus line (Osaka --) Kyoto -- Takayama.
http://www.nouhibus.co.jp/english/kyoto_osaka.html
This expressway bus line is co-operated by Nohi Bus and Kintetsu Bus. All the seats of all the buses on this line require reservation.
The Kyoto Station bus stop on this line is near the Hachijo end [south end] (around Shinkansen tracks) of Kyoto Station Building, not around its Karasuma end [north end] (around Central Gate).
A north-south walkway outside ticket gates is on the 2nd floor of Kyoto Station Building.

Is 3N too many in Karuizawa or 2N will do? We plan to just relax and go slow, what can we do there?

What were you planning to see there? That's a rather long time to spend in a not especially interesting location. If I were you I would stay in the Shibu or Yudakana Onsen area and visit the snow monkeys at Jigokudani.