Does JR pass cover buses?

This is my itinerary for my trip in Dec :
5/12 Shinjuku to Nagano
6/12 Nagano - Shirakawa-go via Toyama - Nagano
7/12 Nagano - Jigokudani Snow Monkey - Nagano
8/12 Nagano - Karuizawa
11/12 Karuizawa - Shinjuku

My questions :
1) Does a 7 day JR Pass cover all my trips?

2) While the JR pass should cover all the Shinkansen trips, will it cover bus trips to Shirawaka-go and Jigikundani Snow Monkey Park?

3) the fare calculator from this website shows a different price per trip as compared to Hyperdia? Hyperdia is slightly cheaper. Why is that so?