Asking for advise

Hi, my husband and I are going to visit Japan for the first time, we will be arriving Haneda on 9/5 (afternoon) and leaving, also from Haneda, on 9/20 (morning).
Here is what our schedule looks like and we are considering getting the 14 days JR Pass.
Would you kindly give us any input/suggestions on our schedule and if the 14 days pass is what we should get?
I read somewhere in the forum that we should use navitime, is this the best tool, what do you think?
Also, if we follow the route from Navitime, will we have enough time to catch the connecting train/s? A friend told us that the stations are big and can be confusing for first timer. Any tip to find our way in stations, since we only know a few Japanesse words, hopefully will be able to learn more by September.
I'm sorry for asking so many questions, but any advise/s are welcomed and very much appreciated.

9/5/2023 Arrive Haneda
9/6/2023 Tokyo - Takaragawa
9/7/2023 Takaragawa - Karuizawa
9/8/2023 Karuizawa - Kanazawa
9/9/2023 Kanazawa - Shirakawago - Takayama
9/10/2023 Takayama - Kyoto
9/11/2023 Kyoto (daytrip to Nara, evening in Kyoto)
9/12/2023 Kyoto to Amanohashidate
Amanohashidate - Kyoto 9/13/2023 Kyoto - Osaka
9/14/2023 Osaka - Beppu
9/15/2023 Beppu to anywhere between Osaka and Haneda
9/16/2023 Stay between Osaka and Haneda
9/17/2023 Stay between Osaka and Haneda
9/18/2023 Stay between Osaka and Haneda
9/19/2023 …................. - Haneda
9/20/2023 Leaving Haneda

Thank you and best regards,
Ingrid