Check Hyperdia or Jorudan for all your train travels. When in Kyoto, check Arukumachi Kyoto website. I am not sure exactly what season is your travel time. I am checking here as well in Japan Guide.
Suggestions:
* If base is Namba, I suggest you to ride Rap:t (fastest) or local train by Nankai from KIX.
*Review Osaka Amazing Pass valid areas.
-It is a good pass yet if you are limited to Osaka Castle and Dotonbori Area make sure that you fully utilize its many perks. Else, much better to combine IC for subway travels (Namba to Osaka Castle and Dotonbori/Shinsaibashi) + Osaka Castle Entrance.
- Osaka Amazing Pass is not valid in Hankyu line going to Minoo. I am not sure what other museum or theatre you will be going to afterwards.
* Day 3:
- Kyoto has several passes as well but if you care to be punctual then ride the trains. Bus is dreading yet economical.
- Are you doing the Higashiyama walk as ending up in Gion?
* Day 4:
- Saga-Arashiyama is JPY 240 away from Kyoto Station.
- Kyoto Station to Inari Station is only JPY 140.
- All JR lines unless you are travelling to other location/line within those areas.
* Day 5: This is a little iffy.
- If you want, you can check the overnight bus from Kyoto to Kanazawa via Nishinihon Bus/Kousoku Bus. Saves you accommodation day. Bus is separate payment.
- Activate on this day your Takayama-Hokuriku Area Pass to use it for the train from Kyoto to Kanazawa (which also includes your bus travels in Shirakawago and Gokayama until Takayama on the following days). It is so good that the problem is that you are only until Takayama by bus or train from Kanazawa.
- If you activate on this day 7-day JR Pass, shell out for the Gokayama-Shirakawago pass or separate bus tickets until Takayama. Or, return to Kanazawa by bus, take shinkansen to Toyama then Wide View Hida to Takayama to fully utilize the JR Pass.
- All bus travels from Kanazawa to Shirakawago and Shirakawago to Takayama are all reserved in advance, whether you hold a pass or not. Check Nohi or Hokutetsu Bus. Shirakawago to Ainokura is a first come, first serve basis (no need of reservation) courtesy of Kaetsuno Bus.
- If you plan to see the coast via bus from Kanazawa station then check Japan Guide to Chirihama Beach Drive
http://www.japan-guide.com/e/e4254.html or here
http://www.hot-ishikawa.jp/kanko/english/20003.html on how to get there. Kanazawa city tour is also something visitors look forward to.
- I assume your base is in Kanazawa.
* Day 6: Travel by bus, ok.
- Will your base be in Shirakawago or Ainokura? I suggest you to be in Shirakawago.
- Tour Shirakawago and Ainokura.
- There is a bus pass called three-star route
http://www.alpico.co.jp/access/ticket/pdf/panf701[1].pdf (add '[1].pdf' if the link omits it after your click). The said bus pass are all bus travels for 4 consecutive days that you can start from either Kanazawa or Matsumoto. In your case, you will start in Kanazawa so have it activated on this day.
- Review the said link. Note that you shell out for another fare/pass from Shirakawago to Gokayama.
- Check Alpico Bus as well.
* Day 7:
- Clarify please. From Ainokura are you going all the way to Nagano and no tour around Takayama and Matsumoto?
- Or this day will be your travel from Ainokura to then tour Takayama and Matsumoto tour prior going to Nagano?
- Take note of the travel times. Ainokura to Shirakawago is more than 30 minutes. Shirakawago to Takayama is 1 hour.
- Takayama-Hokuriku Pass is valid only in Takayama. Ride all the way up to Toyama then pay separate shinkansen ticket to Nagano and local/Shinano train to Matsumoto. Travel time is approximately 3.5 hours.
- The same pass from Takayama then ride down all the way to Nagoya then separate ticket to reach Matsumoto and Nagano. Travel time is 4.5 hours.
- With JR Pass, it's the same train travel except all JR train rides to reach Matsumoto and Nagano are included.
- With bus, it's a direct service from Takayama to Matsumoto for almost 2.5 hours. To reach Nagano is either bus or train from Matsumoto.
- With the said travel times, either forgo Takayama or Matsumoto tour or both.
- Base in Nagano.
* Day 8:
- Your Nagano travels then train to Tokyo.
* Day 9 to 11:
- I am not sure if Tokyo Tokunai or IC will do.
- Day 11 is the end of 7-day JR Pass if you plan to purchase that.
* Day 12 to 13
- Fujigoko/Kawaguchiko Travels. There is a pass covered from Shinjuku round trip. Check here
http://www.japan-guide.com/e/e6905.html.
- There is actually an overnight bus from Mt. Fuji Station or Kawaguchiko station from around 21:00 that will arrive at OCAT (Osaka City Air Terminal, a bus terminal) at around 7:00.
- If you want to go back to Tokyo, there is also an overnight bus from there arriving around 6:30 to 7:00 at Osaka station the next day.
- You can even fly from HND to ITM or KIX. That is, if you plan to sleep in the airport.
* Day 14
- If you ride the overnight bus from Mt.Fuji/Kawaguchiko, you can even catch the bus from there all the way to KIX. Check here
http://bus-en.fujikyu.co.jp/highway/detail/id/9/ and here
http://www.kate.co.jp/en/timetable/detail/OC.
- Fly out of Japan