Hi there!
Here are some answers:
- Nagano - Yamanouchi (I believe it isn't)
Assuming you mean Yudanaka (Yamanouchi is an area), you'll need to use Nagano dentetsu, which is non-JR, to get there. Here's an itinerary.
- Toyama - Kanazawa (am especially confused about this one because I've read that it is and it isn't)
Toyama to Kanazawa is totally covered by JR (and JR Pass). Here is a sample itinerary.
- Odawara - Hakoneyumoto (I believe it isn't)
For this line you will need to purchase separate tickets as the line is run by Odakyu Rail.
Hope this helps!