Hi LAM,
So Kanazawa & Takayama for sightseeing and Nagoya for shopping? Sound good to me!
Let's have a look at your itinerary in a little more detail. Adding a visit to Shirakawa-go is a great plan, I visited the area last March and it was very beautiful. The light-up in the evening is especially wonderful and for this alone it is worth staying the night. If you go for a nights stay in one of the traditional houses, consider arriving the the (after) noon. Shirakawago is very beautiful but also a little small and spending a full day and night there may be too much.
I would also recommend using the bus from Kanazawa - Shirakawago and also use the bus from Shirokawago - Takayama. This way you can save yourself some travel time (instead of going back by bus to Kanazawa and then by rail to Takayama).
As for travel costs, here's a little breakdown of train ticket prices:
Kansai Airport - Kanazawa ¥ 9,540
Takayama - Nagoya ¥ 5,670
Nagoya - Kansai Airport ¥ 8,060
For a total of ¥ 23,300. This would not cover the price of a 7 day JR Pass yet (¥ 28,300). So for now I would recommend buying normal tickets. The bus to Shirakawago unfortunately is not covered by the JR Pass.
For reference if you do take the train from Kanazawa - Takayama it would add ¥ 5,440 using limited express trains.
When you are in Takayama and want to relax at an onsen, consider a visit to Okuhida or Gero Onsen. Both make for great trips!
Lastly if you want to do some last minute shopping before taking your flight back home, visit the premium outlets of Rinku town just one station away from Kansai Airport it makes for ideal last minute shopping.
I hope this helps!
Daniel