Kids Ninja Village to Togakushi Museum?

We are going to take the bus from Nagano to visit the kids ninja village with our 5 and 9 year old boys. Would it be possible to also fit in a visit to the ninja museum and nearby shrine? If so, what is the best way of getting from the kids ninja village to the museum, and how would we then return from the museum area to Nagano?

The structure of the Togakushi Valley is something like below.

D0-D1
|
C0-C1
|
B0
|
A0

A0 is JR Nagano. B0, C0, and D0 are bus stops in Togakushi.

Togakushi Shrine is a set of five shrines. Two shrines near B0, one near C0, and two near D1.
http://togakushi-jinja.jp/shrine/zu/images/map_lrg.jpg
D1 is near Mt Togakushi. It would take 40 minutes from D0 to get there.
http://www.togakushi-21.jp/common/data/kodou_map.jpg

Togakushi Museum is a set of three museums. All are in a single place near D0. The opening hours are 9:00 - 17:00.
https://www.togakushi-ninja.com/

Ninja Village is at C1, 20 minutes on foot from C0. Google says it would take up to 3.5 hours to enjoy there.
It opens from 9:00-17:00.

Most people walk along dedicated paths called Kanmichi, seen in red dotted lines in the first jpg, to cover all the five shrines and three museums in a day. In your case, with small children, it might be better to use buses in Togakushi.
https://www.alpico.co.jp/access/nagano/togakushi/

D0: Togakushi-Okusha
C0: Togakushi-Chusha
B0: Togakushi-Hokosha

For example, if you want to stay about half an hour at each museum or shrine, you could only visit one shrine in the following:

A0(JR Nagano) 830 -(bus)- 934 C0(Togakushi-Chusha) -(walk: 20 min)- C1(Ninja Village/3.5h) - (walk: 20 min)- C0(Togakushi Shrine Chusha/0.5hr) 1439 -(bus)- 1443 D0(Three Togakushi Museums/1.5hr) 1717 - 1818 A0(JR Nagano).

http://www.ninjamura.com/