Hi,
You may not be giving your whole itinerary so it's unclear if the Nagano Niigata Area Pass would actually pay for you. You could get a discounted round trip ticket to Takayama by bus from Matsumoto. The official pages sometimes don't give a clear coverage map, but you can see one with more details on the pass here. Please note that the pass doesn't cover everything, like the last train to see the snow monkeys from Nagano.
You will also be traveling during the end/start of the year. Trains could be quite congested. If you use the pass, it would be smart to make seat reservations - they are free with the pass. Be sure to check if all the places you're going to will actually be open during your trip.
Best of luck.