Grateful for advice on 5 week itinerary

Hello everyone. I'm travelling with my wife (both in our 30s) to Japan for one month arriving on 2 November (just over two weeks from now(!) and unfortunately due to personal reasons we've not managed to fix our itinerary yet!).

It is our first time in Japan and I assume we are in the same position as most people visiting for the first time - we would like to sample as much of the country as possible. Based on our interests we've put together the following itinerary and would appreciate your wise views on whether it is feasible and any insider tips on things we might want to change, or recommendations for accommodation :)
To note, we have not booked any accommodation yet except for the first stage of our Tokyo stay (2-7 November we stay at Shinjuku Granbell Hotel). We will get JR pass (undecided on 14 or 21 days as yet)

2nd: Arrive Tokyo (late at night)
3rd: Tokyo
4th: Tokyo
5th: Tokyo
6th: Tokyo
7th to 12th: Japan Alps/ Central Honshu (Kiso Valley):
We would like to visit Kanazawa and then maybe travel down to Shirakawa-go. I hear Takayama is more touristy these days and we would like to avoid that if possible? Would like to maybe spend a night in Ainokura if possible as it looks a lovely village. Access looks to be only by bus - would you recommend we hire a car for a few days to see the area? Is it worth detour to Matsumoto for the castle?

During this time we would also like to maybe walk the Nakasendo way between Magome and Tsumago - maybe spend an overnight in Tsumago (Fujioto Ryokan looks nice). I am struggling to work out the best way to do all the above after we leave Tokyo on the 7th. Best to go to Kanazawa and then make our way to Magome? Or do the reverse?

13th: Travel to Kyoto
14th: Kyoto (myoshinji Daishin-in temple stay?)
15th : Kyoto
16th: Kobe/Osaka (are these worth more than a day trip from Kyoto?)
17th: Koya-san (temple overnight stay? Is Koya-san area very touristy? If so, any better place for a temple stay with fewer tourists - we are looking at Gyokuzoin temple in Shigisan, near Nara.
18th: Koya-san (Koyasan Choishi pilgrimage trail hike?)
19th: Nara (worth spending another night here?) Gyokuzoin temple stay?
20th: Hiroshima (stop off in Himeji en route)
21st: Hiroshima
22nd: Miyajima
23rd to 29th: Kyushu: We thought it would be nice to spend 6 days travelling around Kyush, maybe with a hire car. I would appreciate any recommendations on what to do here. Is it worth spending a few days in Fukuoka and Nagasaki? Is Kumamoto still worth a visit after the earthquake last year? Are there any areas to avoid after the aso-san eruption?
We would like to stay a night in one of the Kurokawa onsen if possible. Any recommendations for good day hikes in the region? We thought maybe Kirishima.

30th Nov to 5th Dec: Tokyo - Sumo stable, Maricar go kart tour :)

Thank you so much for any and all help! Much appreciated!

I hope you are aware that the second half of November is peak season for fall colours in Japan and accommodation can be tight and expensive especially in Kyoto.

So I advise you to look into accommodation for this period as soon as possible especially if your dates for the Kansai region are fixed. If you don't find affordable accommodation in Kyoto during this time, you can book in Osaka and commute between the two, it's only about 30min or less by local trains (depending on where you want to go in Kyoto and where you stay in Osaka).

Just out of curiosity, why do you want to experience 3 temple stays? One in Koyasan, one in Kyoto and one in Nara?

"Just out of curiosity, why do you want to experience 3 temple stays? One in Koyasan, one in Kyoto and one in Nara?"

This is a good question. I've found Koyasan to be a good place to stay in a temple which is accessible to english speakers....

You mention that you are in Kyushu at end of November and you also seem to be interested in Sumo. Actually the Sumo tournament is in Fukuoka in those days. I am not sure if you can still find tickets, but you can try. There is a web page in English where you can buy them and pick up at a 7/11. The webpage is something with Pia in its name.

Enjoy your trip to Japan!