First time in Japan - help with itinerary

My daughter is going on a school trip to Japan this June and we are taking the opportunity for a family trip beforehand. I have never been to Japan, so I am just starting to orient myself and develop a tentative itinerary. We are a group of 3 adults and 3 kids (my husband and I, both daughters 14 and 17, and another dad and his daughter also 14).

We will be there about 10-14 days before meeting up with the group in Tokyo. We will drop the girls off and then spend another couple days in Toyko before flying home. I am including the school trip itinerary because I don't want to duplicate.

School Itinerary highlights:

Tokyo - Imperial Palace Plaza, Asakusa Kannon Temple, Nakamise Street, Tokyo SkyTree Tower, local fish market - make sushi

Mt Fuji

Tea Farm (on the way to Nagoya)

Nagoya - Atsuta Jingu Shrine

Kyoto - Kiyomizu-dera Temple, Kinkakuji (Golden Pavilion), Fushimi Inari Taisha Shrine

Nara -Todaiji Temple, Nara Park, Kasuga Shrine

Osaka - Osaka Castle, CupNoodles Museum, Kuromon Ichiba Market

For our trip, I was wanting to pick just a few places to stay anywhere from 2-4 nights (I don't like jumping around too much and like to put down roots in one place to get a better feel for an area). We enjoy food, nature, light hiking, and cultural experiences. Since the school group is touching on more touristy places, I wanted to focus more on off the beaten path and nature. Every though the school trip goes to there, I have been told not to miss Kyoto so I have included it and it�fs a good place for day trips.

A very tentative plan would be to fly into Osaka:

Kyoto 4 nights - day trip to Himeji

Kanazawa 3 nights

Takayama - 3 nights, stop in Shirakawago on the way

Tokyo - 4 nights (maybe day trip to Nikko)

Fly home from Tokyo

Any other suggestions on places to travel? I feel like I might be missing an opportunity to visit more rural areas or more nature areas? Any recommendations for scenic drives?

Thinking of taking a train to Kyoto and Tokyo but driving to Kanazawa and Takayama. I�fm worried about public transport traveling with 6 people including 3 kids and we generally aren�ft light packers. I�fm more open to trains but generally don�ft like buses.

One less day for Kanazawa and Takayama. One more day for Tokyo and Kyoto.

Oh you'll have no issues with public transport. You ain't a large group.

If you are thinking driving Kyoto - Kanazawa -Takayama - Tokyo that�fs a LOT of driving and you drop the car far away. Which will be expensive.

I would do all this by train (faster / easier) but rent a car in Takayama for 1-2 days to explore more rural places (Ainokura, Hirayuonsen) as day trips.

Since you plan to drive around Kanazawa, you can consider visiting Kaga Onsen. Yamanaka Onsen is particularly nice.
https://visitjapan-vegetarian.com/kaga-onsen-the-charming-onsen-resort...

From Kyoto, you can also consider visiting Amanohashidate + Ine Bay for an overnight trip.
Amanohashidate:
https://visitjapan-vegetarian.com/amanohashidate-one-of-the-three-view...

Ine Bay:
https://visitjapan-vegetarian.com/ine-bay-an-amazing-fishing-town-nort...

You can also consider visiting Shiga Prefecture, next to Kyoto
https://visitjapan-vegetarian.com/the-best-attractions-to-visit-in-shi...

I�fm getting close to at least making my plane reservations and my final itinerary may change a little depending on airfare and which days are best to travel.

We will defintely take trains from Osaka to Kyoto, Kyoto to Kanazawa, and Takayama to Tokyo. However, we may consider renting a car in Kanazawa so we can explore the Noto Peninsula one day and return the car in Takayama after exploring the more scenic areas. We love driving scenic routes while visiting different places.

And instead of Himeji Castle we may consider stopping at Matsumoto castle en route to Tokyo and so we don�ft have to worry about bags forward our luggage from Takayama to Tokyo.

Revised itinerary:

Fly into Osaka, train to Kyoto, 4 nights - day trip to Hiroshima/Moyajima

Kanazawa 3 nights - 1 day in Kanazawa, rent car, one day exploring area, maybe Noto peninsula if recovered from earthquake.

Takayama - 3 nights, drive scenic route, stop in Shirakawago on the way, explore rural areas

Train to Tokyo (maybe forward luggage??) - Matsumoto castle on the way, 4 nights (maybe day trip to Nikko)

Fly home from Tokyo

Best car rental with the most options? I looked at one site and the larger minivan type car that could fit 6 people plus luggage wasn�ft available rent in Kanazawa and return in Takayama. Is there any kind of loop trip that makes sense to explore near Takayama then return car in Kanazawa before getting train to Tokyo? Or drive from Takayama towards Tokyo and drop car in nearest larger town?

Takayama -Matsumoto would be bus & train. Then train from Matsumoto to Tokyo.

Noto peninsula I doubt that it will have recovered enough for tourist visits. Other apps suggested otger good areas in Kanazawa area.

Maybe drive from Takayama to Matsumoto (google says it�fs just two hours and I assume maybe a little more) then drop the car after?

Or in terms of accessibility, is it easier to not see Matsumoto and go back to visiting Himeji while in Kyoto. Is it easy to travel by train from Takayama to Tokyo?

Himeiji from Kyoto is easier access than Matsumoto.
But driving Takyama to Matsumoto you come through some nice mountain landscapes and onsen villages. You could even visit Kamikochi
Sorry i don�ft remember when you go. If after mid April before mid Nov driving should be fine. Otherwise you might have snow/ice.

Dropping off car in different prefecture is expensive and as you saw not so easy to find offers. I would try with the bigger rental agencies such as Toyota , Nissan�c maybe they offer drop off after away.

I have read in another thread that it is easier to do Kyoto -> Takayama -> Kanazawa -> Tokyo, because there's a direct bus from Kyoto to Takayama, and a direct train from Kanazawa to Tokyo. The long distance bus usually have enough space in the hold for your suitcases. The bus should also stop once or twice midway for a toilet break in rest areas.

You could rent a car for 2 days in Takayama, return it there. Then go to Kanazawa, and rent another. From what I have seen, the price doesn't decrease whether you rent it for 2, 3 or 4 days.

I saw that your daughter's itinerary already includes it, but if you go to Kyoto, it would be sad to miss Kiyomizu-dera.