Hi there!
Wow! Looks like a great trip! Here are some thoughts for you:
Bus from Aso to Kurokawa
The Kyusanko bus from Mt Aso to Kurokawa onsen will cost ¥1500. You can see the following timetables for departures (from Aso Station to Kurokawa onsen) here and here (google translate). You should certainly contact the tourism information desks at Aso station who will be able to offer further help on this. They do speak english so you should get a lot of great tips that way:
- ASO Information Center. tel.0967-34-0751 (9:00-18:00; Telephone service is not available on Mon. & Thu.)
- Aso Volcano Museum Information Center tel.0967-34-2111 (9:00-17:00)
If you do go to Kurokawa, you should certainly use the lockers at Aso station to store your luggage and go and see the volcano if you have time!
Bus from Matsumoto to Takayama, and from Takayama to Kanazawa via shirakawago
[Reservations are not required for the Matsumoto-Takayama line], but it's worth bearing in mind that it will be first come first served so you should arrive well in advance of travel.
[For the Takayama - Shirakawago - Kanazawa bus, certain buses do require reservations]. I think this line is likely to be quite busy so I recommend calling ahead and reserving your tickets. You can call the Nohi Bus Reservation Center on +81 (577) 32-1688 between 9:00-18:00 JST.
Best use of the JR pass
As you'll be travelling by bus from Matsumoto to Kanazawa I think you've got the right idea to start your JR Pass validity on the 9th. If you can move one day in Tokyo from the end of your trip to the start at the start you will be able to also include the trip back to Narita inside the JR Pass, but aside from that small modification I think you're plans are good.
Tips for Tokyo
As you'll be doing a lot of travel in Tokyo, I recommend you look into the [Keisei Skyline + 2 day unlimited metro pass] deal for your travel from/to Narita Airport. You can also purchase further special discounted 2 day metro passes at Narita working out at ¥490/day. (note these discounted metro passes are only available at Narita Airport).
Hope this helps!