Oct-sep Trip (Need advice)

Hello! I am 21 from Australia
I plan to visit Japan for the first time, over september and october for about 4 weeks, but i haven't fully planned out each place i will go to because apart from Tokyo and Kyoto i am not sure where to go to.

Current plan is

Tokyo 1 week (Based in Asakusa)

Areas near Japan alps days unknown

Mt fuji

Kyoto 1 week

places around kyoto

My ideal places to visit would be of course the main cities but i would like to go to the more rural parts of the country to see shrines, mountains and go hiking.

Budget wise, ill have enough to spend on a low-medium budget.

My main problem is how i am going to travel to each place if it is not covered by the JR rail pass and where would i stay in the more rural places.

Language wise i will do a short course to help me understand the basics of the language.

My main goal is to experience Japan as best i can from all aspects. I just need recommendations mainly on travel and the main places in Japan that are a must for anyone visiting there.

I will be grateful for any input, thanks in advance !

I meant Sep-Oct

Week 1: Hokkaido/Tohoku

Sapporo
Hakodate
Aomori
Lake Towada/Oirase Gorge
Sendai (Matsushima Bay-Ishinomaki)
Nikko

Week 2: Kanto

Tokyo
Kamakura
Yokohama

Week 3: Kansai

Kyoto
Osaka
Nara

Week 4: Chugoku

Himeji
Okayama
Hiroshima
Miyajima
Matsue

Maybe something like that? You could venture into Shikoku from Okayama or into Kyushu. I'm seeing all 4 islands in 29 days. It just depends on how much time you want to spend in each place and/or how much you're willing to spend on trains, time-wise. How many passes/days will you have?

For a first trip, heading all the way to Hokkaido might use a bit too much time, and will be more challenging than the more central areas (even for a four week trip).

Spending time in Tokyo at the beginning is a good introduction - it is a bit more expensive than some of the other areas, but there is a lot to see there.

Heading to Kyoto (more temples and culture) you can easily spend a week or more there. It is a good place to sty, and with limited language and budget you can do pretty well.

For your other weeks, head further south - you could go to Nagasaki (it's nice), or west to Kanazawa via the mountains.

Heading too far away from the main cities or main tourist attraction cities will not be a good idea for first timer and if you do not understand the language. The further you move outward, do be aware that the chances you will be able to use your English will decrease exponentially...

Focusing on Kanto and Kansai will be good start. Most importantly, what do you want to visit Japan for? What do you want to see most? or what you want to experience etc? To be fair, Tokyo itself is huge and you can easily spend quite a considerable time there.

Try narrow down on the purpose of your trips and we could probably give you some ideas where would be good to go.

I personally find that Tokyo has a bit of everything. Although, good for a short trip if you are there for that many weeks you can go to other parts of Japan. I always feel that Tokyo is confused; it has too much cultures mixed together.

Since you have the time, you can go to Osaka for electronics and savoury food; Kyoto for traditions and haute cuisine; Fukuoka for Ramen; Hokkaido for cakes, sweets, and pastries; and some place for hot springs.

If you are already experiencing the various best parts of japan in their main stay cities, there is little reason to stay in Tokyo that is just a mesh of them all. Except for seeing skyscrapers and having a city feel. Though, Osaka city and Kobe night view is sufficient.

I would spend 1 week in Hokkaido. Traversing from Shiretoko to Hakodate. Stopping along Daisetsuzan, Toya lake, Otaru, Noboribetsu onsen, and one of the national parks.
Use Hokkaido rail pass, or drive. Or use a tour company.

Use 7 JR Pass
From Hokkaido, take train to Hirosaki. Stay the night. Strolling along the streets of this quaint castle town just to relax and break the journey.

Spend some time in Yamadera, Ginzan onsen, Matsushima. 5 days allocation should be sufficient.

Go to Kanazawa via Tokyo
Pass ends
Spend 3 - 5 days in this area. Taking side trips from Kanazawa to Fukui onsen, Takayama, Shirakawago, Toyama, Nagano.

Train to Kyoto
Spend a week here
Use one day to go to Osaka
Rest of the time should be spent in Kyoto

Usage of Overnight coaches is recommended if on a budget.

Coaches travels to various cities and you could get a bus pass too.

From Kyoto going to Hiroshima and stopping along the way to Kobe, Himeji, Okayama if they interest you.
Hiroshima should be 2 days long.

Spend last week exploring northern Kyushu. Nagasaki, Fukukoka, Beppu, Kumamoto, Aso, Yufuin. Use SUN Q Bus Pass or JR Kyushu pass.

Any extra time available could be used spent in Tokyo, or relaxing in an onsen town. Just chilling and getting rid of those sores/aches from massive travelling.
Kansai and Kyushu has many great onsens.
Urashima hotel, Suginoi hotel, Daiichi Takimotokan...

Otherwise, a 3 weeks itinerary could look like this... From some of my trip and what i researched etc

1.Tokyo
2.Tokyo
3.Tokyo
4.Tokyo
(Tokyo surrounding has many places to explore outside eg. Nikko, Kamakura etc)
5.Hakone (or Mount Fuji)
6.Hakone (or Mount Fuji)
7.Kyoto
8.Kyoto
9.Kyoto
10.Kyoto
(You can mix Nara, Hikone, Osaka, Koyasan in Kyoto part but Kyoto itself has a lot to offer, increase the date as needed)
11.Kobe (with Himeji castle) overnight
12.Hiroshima (with Miyajima) overnight
13.Okayama (One of the 3 garden) overnight
14.Matsue (Izumo Shrine) overnight
15.Tottori
16.Kyoto/Osaka (R&R as needed)
17.Kanazawa (I like Kanazawa so I would put 2 days, reduce as necessary)
18.Kanazawa
19.Takayama
20.Takayama? (worth 2 days Takayama if you keen to go Shirakawa-go)
21.Nagoya (Just to visit more place and if you want to check the city out otherwise just take bus from Takayama straight to Matsumoto)
22.Matsumoto (One of 12 original castles)
23.Nagano
24.Karuizawa
25.Tokyo
26.Tokyo
27.Tokyo
28.Tokyo
(Finish up with R&R in Tokyo or you can move Northwards to Sendai etc)

That's about 28 days trip, just adjust, add subtract as needed, use this site to check on places I've included to see if it's your taste.