Please advise on my itinerary

What time of the year are you travelling? This could make a big difference for nature places.

Based on the below itinerary, would I need to a Jrail pass?

Doesn't look like a JR pass would make sense. Perhaps one of the regional rail passes could pay off.

3 DAY TRIP TO IBARAKI, FUKURODA FALL, KAIRAKUEN PARK, MT TSUKUBA

Not sure, but this might be one sight too much for one day.

4 TSUKIJI, MEIJI SHRINE, SHINJUKU GARDEN, RIKUGIEN, KOISHIKAWA KORAKUEN

I would not bother with Shinjuku Garden ("gyoen") which is mostly just a regular western style park. It is a good place for a picnic, but with little time in Japan I would focus on more Japanese things. Rikugien and Koishikawa Korakuen are fine gardens for Tokyo but you will see equally good and better in Kyoto. Same for Meiji Shrine and Asakusa/Sensoji. Really in Tokyo I would focus on things it is good at, i.e. mostly on modern ctiy stuff. Also, each of these places is in a different part of Tokyo, and you will spend considerable time moving from one place to another. In one day, I'd try to cover one or at most two parts of Tokyo and do a lot of walking.

5 DAY TRIP TO KAMAKURA
6 MT FUJI, KAWAGUCHIKO, CHUREITO PAGODA

All good day trips from Tokyo, but personally I'd rather have two days in Nikko (which has better nature and very good shrines/temples). I'd most likely sacrifice the Tsukuba and Kawaguchiko day trips for it.

7 SAIKO, TRAVEL TO MATSUMOTO LATE AFTERNOON VIA KOFU AND SPEND NIGHT IN KOFU
8 SHOSENKYO GORGE IN KOFU AND SPEND NIGHT IN MATSUMOTO

I don't understand this part. Why do you go twice (on day 7 and 8) to Matsumoto?

9 MATSUMOTO CASTLE & JOYAMA PARK, SHIRAHONE ONSEN IN THE AFTERNOON
10 SHIRAHONE ONSEN BACK MATSUMOTO VIA SHUTTLE BUS, MATSUMOTO TO TOYAMA VIA NAGANO, MONKEY PARK IF TIME ALLOWS, SPEND THE NIGHT IN TOYAMA

If you can skip the monkey park, you could travel Shirahone Onsen-(Kamikochi)-Takayama-Toyama instead

11 KUROBE GORGE (EXPECT 11 NOV)

Could probably do something else on this day, or at least go to Kanazawa.

12 TOYAMA TO NAGOYA VIA KANAZAWA, KENROKUEN IN KANAZAWA, HIMI COASTLINE IN THE MORNING

13 DAY TRIP TO KORANKEI VALLEY, OBARA IF TIME ALLOWS

Places like these are fine if you have the time, but I'd rather have more time in Kyoto

17 HALF DAY NARA, HALF DAY UJI

Nara has enough to keep you busy for a day or more. I would not try to split time between Nara and Uji as you'd lose around 1 hour or so on transport.

18 KYOTO
19 KYOTO TO SHINGU, KUMANO KODO
20 DAY TRIP TO NACHI FALL, HONGU
21 SHINGU TO ISE SHIMA, VISIT ISE GRAND SHRINE
22 TOBA, AMAHUT, ISE BACK TO OSAKA LATE AFTERNOON

You could investigate whether it would make sense to travel this in reverse direction after Nagoya/Kiso Valley.

23 DAY TRIP TO KOYA SAN

The main point in Koyasan is the temple stay/early morning service. IMO you lose a lot if you go just for a day trip. The temples themselves are not all that special compared to what you can see in Nara or Kyoto.

I don't think a JR Pass is going to make much sense for you, but you'll have to do the calculations yourself. Note that on many occasions you will be traveling by methods other than JR trains.

Your itinerary is a little odd, in places. I don't understand you jumping back and forth between Matsumoto and Kufu. Also, the way you combine Nagoya with everything else makes no sense. Do you fly out of Kansai Airport? If so, leave all the Kansai stuff for the end. Head from Kanazawa to Nagoya, from Nagoya to Ise, from Ise to the Kumano region, from there to Koyasan, and then Osaka/Kyoto at the end. That would make a lot more sense.

Kanazawa is a great city, and deserves more than a few hours.

I've driven nearly all the way to Himi before, and can't really see it as a highlight of Japan, certainly not on a short trip. What do you want to do there? There are some obscure historical sights on the way there, and then beaches, which will be dead in winter (unless the surfers are super, super keen). It's not that scenic, certainly not scenic enough to go out of your way to see. With spare time, hang around Takaoka itself instead.

Anyway. Your itinerary is pretty rushed (read that as too rushed), but I'm sure you know that...

I agree there is a lot here. Much of it seems to be traveling for the sake of traveling, spending a lot of time on trains for day trips, and criss crossing around central Japan rather than taking a straight route and seeing what is on the way.

Koyasan for a day is silly. So much time in transport and you miss the exprience people go there for, the solitude at night.
Passing through Kanazawa but not seeing it seems strange.
The Matsumoto, Kofu, Nagoya section confuses me to no end. Why anyone would set their itinerary up like that?

Many thanks for the great and details response everyone.
I will arrive in Tokyo on the 21st of November and departure is on the 16th of December.
Like I said I found this itinerary and looked interesting and I picked it, I am happy to change wherever it makes sense and feasible. I am more into nature scenery than cities or temples.

Ho would i fit in the below, I mean in what order and does it make sense?

Kanazawa, Shirakawa-go, Takayama, Kamikochi and Matsumoto

Matsumoto-Kamikochi-Takayma-Shirakawa-go-Kanazawa is the only order that makes any sense.

I think Kamikochi will be closed already by the end of November; it's easy enough to check the opening dates online. But it closes for the winter.

I will arrive in Tokyo on the 21st of November and departure is on the 16th of December.

Late November/early December has autumn foliage at low altitude/coastal places like Tokyo, Kyoto. Other than that, in my experience it is not a great time for nature in the mountains as vegetation will be bleak and higher altitude places closed.

Like I said I found this itinerary and looked interesting and I picked it, I am happy to change wherever it makes sense and feasible. I am more into nature scenery than cities or temples.

I agree with the other posters above, that it is quite a fast itinerary and I'd seriously consider slowing down a bit skipping some places in favor of more time elsewhere.

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