Stops in Matsumoto & Kanazawa?

Will be in Japan for 2 weeks late September, arriving in & departing from Tokyo. Looking to save Tokyo for the last 4 days of our trip & trying to organize the rest.
Want to spend a few days in Kyoto and figure out travel (before or after Kyoto) to see Matsumoto & Kanazawa.
Can anyone help me with organizing the best plan of action?
And any other suggestions of any kind based on the above info would be really helpful as well.
Thanks!

We are visiting in September also, and are planning the following as part of our trip:

Day 9 Morning train Kyoto to Kanazawa.
Day 10 Kanazawa; early afternoon bus to Takayama via Shirakawago which will give us a brief glimpse of this village.
Day 11 Takayama
Day 12 Early bus to Matsumoto to see the Castle; afternoon train to Tokyo.

A bit rushed but hopefully a worthwhile visit to each place!

I would disagree.
Kanazawa requires no less than two full days

Whether you plan to stay in Takayama or Shirakawago makes no difference. However, I would just go to Takayama in the morning and Shirakawago in the afternoon. You can do both in a day and then head onto Matsumoto

Steven, sorry to hijack your question.

I hope people will have more advice.

How many days you will have for Matsumoto and Kanazawa?

September will still be reasonably hot, and not a particular foliage season, so timing of visits will be less of an issue.
Assuming you will have a JR Pass?
Depending on how you use it, a 7 day pass pays off with a Tokyo/Kyoto return, and if Narita is included then even more so.
A 14 day Pass will pay off for 14 days withTokyo/Kyoto return, Narita airport, with decent length side trips.
Not sure what time you arrive in Tokyo, and whether it is Narita or Haneda.....

All this advice is assuming a 14 day JR Pass, and maximizing its cost

1. Matsumoto can be a day trip from Tokyo: Shinjuku Matsumoto return on the Super Asuza is an easy day trip: we have done it twice, and on one occasion then went from Matsumoto to Nagano and back to Tokyo by Shinkansen.
2. The new Hokuriku Shinkansen opens up other options:
eg: Shinkansen from Tokyo to Nagano, then Limited Express to Matsumoto: maybe stay overnight
then Matsumoto back to Nagano, and off to Kanazawa by Hokuriku Shinkansen
OR Matsumoto to Kyoto via Nagoya
3. Matsumoto as a side trip from Kanazawa by the Shinkansen etc
Note: Kanazawa alone needs at least 2 full days: Kenrokuen, 21st Century Museum, Gold leaf shop and tour, Geisha area, Samurai area, Ninja dera: 2 days: .....
4. Wajima and Noto peninsular IF time allows on a 3rd day. Suggest Hokutetsu day trip: narrated in Japanese, but still worthwhile.
5. Shirakawago is a wonderful day/half day trip from Kanazawa, nothing quite like it.

Once in Kyoto
6. Need at least 2-3 full days to cover all �gTHE�h major sights in Kyoto:
7. Nara is a great day trip from Kyoto
8. Mt Koya is also a wonderful day trip/overnight possibility
9. Himeji Castle is iconic, and an easy day/half day trip from Kyoto
10. It is possible to go to Hiroshima/Miyajima as a long day trip from Kyoto
11. Osaka?? fun for shopping, night life and food.....we actually stay in Osaka and do day trips to Kyoto from there, as we always have a Pass

Once back in Tokyo
11. 4 days in Tokyo itself won�ft be hard to fill...you may not need to go anywhere else
12. Nikko is a full day side trip
13. Kamakura can be a half day trip

So the possibilities are endless:

Maybe post arrival and departure times and airports, and we can help more from there:

Many thanks for the detailed info! And sorry I wasn't more clear in my original post.
We'll be landing in Tokyo on Sept. 25 early afternoon. Plan to stay 1 overnight in Tokyo before heading to Kyoto on the afternoon of the 26th. Have reservations at Hotel Mume for 4 nights, so plenty of time to enjoy Kyoto & surroundings.
I wasn't sure how best to handle travel to the other destinations prior to our return to Tokyo. We'll most likely have from Sept. 29-Oct 3 to explore the smaller towns (Kanazawa, Matsumoto & any other recommended). So would like to know how much time is needed in each spot & if choosing a "home base" might be better than bouncing from one to the next.
Thanks again in advance!

And, sorry, we're flying in and out of Narita.
So you think a 14-day JR Pass is our best bet for all this zipping around??
Thanks.

I think your travel route should be as follows:

Narita AP to Tokyo (JR, Keisei or bus)
Tokyo to Kyoto (Shinkansen)
Kyoto to Kanazawa (JR)
Kanazawa to Takayama (bus, probably stops at Shirakawago)
Takayama to Matsumoto (bus, probably stops at Hirayu onsen and Kamikochi)
Matsumoto to Tokyo (JR)
Tokyo to Narita (JR, Keisei or bus)

I just calculated the JR part of the itinerary which turned out to be around 35000 yen, about 10000 yen cheaper than 14 day JR Pass. As AusTF stated you must add some side trips to justify the JR pass. Maybe Nikko or Karuizawa from Tokyo or Hiroshima from Kyoto/Osaka.

By the way, if you do Kanazawa Takayama Matsumoto part by bus within 4 days, you might better look at Mitsuboshi route Kippu

https://www.alpico.co.jp/access/ticket/matsumoto_kanazawa.html

which covers this route and somewhat cheaper than buying individual tickets. You can buy it at Hokuriku Tetsudo Kanazawa Ekimae Center.

Now that sounds like a plan!
To be honest, it's almost worth the extra cost just to have the ease of use with the JR Pass. The idea of purchasing individual tickets for each trip makes me cringe. If we do one or two 1/2-day trips when in Tokyo, also might make it more worthwhile.
Thanks again.

If you take JR Pass, you might better reserve your seat. It can be done in any major JR station such as Narita airport, Tokyo, Kyoto, Kanazawa and so on. Upon reservation you should prepare printed images of hyperdia: the staff at the ticket booth should be very used to read it: just number your first, second... choices on the printed sheet.

You must reserve the highway bus from Kanazawa to Shirakawago and Shirakawago to Takayama. You can reserve your seat at Kanazawa when you buy the ticket. As for Takayama to Matsumoto part, you don't to need to/can't reserve the seat.

So now just considering another option for our 4 open days prior to heading back to Tokyo...
If we decide to head South rather than North from Kyoto, what is the area like around Osaka & Kobe? Worth the time?... or better to stick to our original Kanazawa+ plan?
We were originally going to head over to stay in Fukuoka for a few nights, but thought it might just be too far out of the way...
Thoughts??
Thanks.

I assume you have 8 nights left after spending 4 nights in Kyoto and you will have 14 days JR pass. You will have 3 full days in Kyoto which is enough for many tourists.

I will post a draft plan for your 8 days. Of course, people are different and you must have your own preference, so, this is for just MY pleasure :).

Day 1 Day trip to Nara from Kyoto. Night at Osaka.
Day 2 Hiroshima and Miyajima. Night at Miyajima.
Day 3 Early Shinkansen to Shin-Osaka and then limited express to Kanazawa. Night at Kanazawa.
Day 4 Explore Kanazawa. Night at Kanazawa.
Day 5 Morning bus to Shirakawago. Explore Shirakawago and evening bus to Takayama. Stay at Takayama.
Day 6 Explore Takayama. Afternoon bus to Hirayu Onsen and then to Kamikochi. Stay at Kamikochi.
Day 7 Explore Kamokochi. Afternoon bus to Hirayu Onsen and then to Matsumoto. Matsumoto castle. Evening train to Tokyo. Night at Tokyo.
Day 8 Explore Tokyo. Night at Tokyo.
Day 9 NEX to Narita.

If you want to experience many aspects of Japan, the following places are specifically important: Kamikochi (mountain, clear river). Miyajima (sea shore). Shirakawago (country side and old wooden houses).

Hope this helps.