Is the JR Pass valid on these routes?

Hi there!

Here are some answers:

1. 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.

1. 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.

1. 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!