You easily make a 2 week pass pay off for the fist 14 days of your trip, and with a side trip from Tokyo for example to Nikko you'd make a 21 day pass pay off, but a few issues.
First, why go from Kanazawa to Tokyo and then backtrack to take the Tateyama kurobe alpine route? Why not just go from Kanazawa to Toyama?
Secondly, what airport are you leaving Japan from? Sapporo or Tokyo? Why kill yourself by taking a train from Tokyo to Hokkaido? It's over 9 hours from Tokyo to Sapporo, killing a while day. Or about 5½ just to Hakkodate, but that's still a long ride. You might consider getting a 2 week pass and then flying to Hokkaido from Tokyo. You can fly very cheaply these days with a low cost carrier like Jet Star for as low as ¥4,190 and get there in about 2 hours. Another option is [ANA's Experience Japan Fare]. In Hokkaido it depends on where you plan to travel of course. You could be using a 3 week JR Pass, pay regular fare after a 2 week JR Pass, or use a Hokkaido Rail Pass.
Starting from the south, both Fukuoka and Nagasaki have some great sightseeing. In Fukuoka don't miss the Nanzoin Temple and try the Hakata Ramen at the Nakasu Yatai Stalls. You can get some good sightseeing info here, and see:
https://www.youtube.com/playlist?list=PL7LcPcmoSg-j4RLa6iC7ayvBAbOn8-028
https://www.youtube.com/playlist?list=PL7LcPcmoSg-gbw2yXNLK92siHyNqSNxXz
For the Kansai area, don't miss seeing Himeji and Nara. For the Tokyo area, take some day trips also to see Nikko.