Hi there!
Looking at the your planned route, I think that it would be best to travel using normal tickets. This because most of your travel from Takayama - Shikarawago and Ogimachi in addition to Jigokudani is mostly covered by bus and private railway.
When you arrive at Narita Airport, consider buying a [Suica + Narita Express package]to get a discounted ticket on the Narita Express and a prepaid travel card (Suica) which you can use to pay for local travel in Tokyo and other parts in Japan.
Enjoy Japan!
Daniel