My Itin vs JR pass

Hi,
Given the length and destinations in your trip, a JR Pass would unfortunately not work for you. I suggest you get regular tickets. As for the bus, train or shinkansen, that is entirely up to you. The shinkansen of course does not go everywhere, and as for using a train or bus, the bus is of course much cheaper but the bullet train (and often the train) is quicker. For getting to NIseko, Shirakawago, and Nagoya Airport (Centrair) you have to take a bus.

You can get more info on getting to NIseko here, and for Shirakawago here. A regional pass might help you with some of your trip, such as the Takayama-Hokuriku Area Tourist Pass.

Please also be aware that you are traveling over New Years. At the end of the year and the start of the New Year, many places are closed. Be sure to check if where you are going will be open or not. Trains could also be very crowded. This is one of the times when getting a ticket with reserved seating makes a lot of sense.

Regarding the plans themselves, you are giving very little attention to Kyoto. You might consider largely skipping Nagoya, and using that time to see more of Kyoto, or even Nara.

Best of luck.