Help with Itinerary Planning

Hi, we will be in Japan for about 40 days in late December 2018/January 2019 and need help deciding how to best use the JR pass and which JR pass combinations make the most sense for us.

First, we will be flying into Narita and exploring Tokyo for 3 days. Then, we will be flying to Sapporo (reservations already made) and heading to Furano from the Sapporo airport. 6 days later we will head to Asahikawa. 3 days after that we will go to Niseko. 5 days after that we will go back to Sapporo, and 2 days later fly back to Tokyo. After arriving in Tokyo, we will go to Kyoto for 5 days. Then, we will head to Hakuba for 4 days, then to Myoko kogen for 4 days, the to Nozawa Onzen for 3 days and then finally back to Tokyo.

It's hard to know from the website which of these routes are covered by the JR pass and which pass combination we should purchase. Can you help us organize our travel in between each of these destinations and determine the best pass options?
Thanks,
Brandon and Larissa Thompson