Hi Fliss!
Yes Hyperdia can indeed a little confusing at time! Even I get confused a little from time to time with all the information available. For Tokyo, simply use "Tokyo", here you can find an example route between Tokyo and Shin-Kobe, feel free to change to time at the bottom of the page.
About Ginza, it is an area very close to Tokyo station and you can walk from Tokyo station to Ginza in less than 10 minutes. However all Shinkansen to Kobe leave from Tokyo station.
Kobe is a very nice place to start, I visited the city this year in January and it made for a great time, if you have time go up mount Rokko which makes for a beautiful sight, especially after dark, you can see the whole of Kansai lighting up. From Kobe you can reach Takayama with a transfer at Nagoya. Here is the route. I meant that there may not be enough time to visit both Kanazawa and Shirakawa-go, so I would recommend visiting one. Shirakawa-go makes for a great day trip and can be reached by express bus from Takayama. It is not too hard to go back from Takayama to Tokyo, here you can find the route.
There was a lot of information in your post, so I hope that I covered everything. You can find the reverse time table by pressing the little button in Hyperdia that has a double arrow.
Hope this helps,
-Daniel
PS: One last tip, if you are looking for an accommodation in Kobe, stay in the Sannomiya area, this is the heart of Kobe and is home to many wonderful places.