No such pass.

JR Rail Pass covered Shinkansen from Tokyo to Osaka and Kyoto but JR train coverage in Osaka , Kyoto and Tokyo are crap, suxk.  JR Rail Pass totally useless in Hakone. Kawaguchiko only Limited Express "Fuji Excersion"

Best pass for Osaka and Kyoto will be Amazing Kansai Pass but this pass cannot take JR train.

Tokyo are fully covered by Metro. 3 day unlimited metro pass will be the best but you can't take JR , Keikyu , Odakyu train.

Fuji will be Odakyu Fuji Free Pass.  It covered entire Kawaguchiko and Hakone but you only limited to Odakyu.

JR pass not worth it if you just travel one way from Kyoto to Tokyo. JR Rail Pass cost Rm1.4k for 7 days.

Please google more on Kansai Amazing Pass.

Depends on your journey… the Japan Rail Nationwide pass is only worth it if you travel many cities in a short time
And bad thing is JR stations are limited in cities

E.g. It’s worth it for me to get the 14 days JR pass because I’m doing
Tokyo - Nagano - Toyama - Takayama - Osaka - Kyoto - Nara - Hemiji - Tokyo

It depends how much you are traveling each day. If at relax pace and just 1-2 places/day. It's much cheaper and convinient to use SUICA/PASMO card (works just like TnG card on LRT/MRT)

Tokyo metro 1/2/3 days pass are not really worth it unless your hotel are next to subway station as this pass cannot use on JR Yamanote line which is very convenient ( circle line)

Think of this metro pass as a special pass in KL that can take unlimited monorail but cannot use on LRT/MRT. Very limited locations and you won't repeatedly take unless your hotel is at Berjaya Times Square.

Osaka Amazing Pass is only for Osaka and only have 1-day and 2-day options. Both covers Osaka subway, tramway, and bus only but the 1-day version gives more choice of lines to use.

Are you referring to Kansai Thru Pass instead? https://www.japan-guide.com/e/e2357_005.html

Both not valid for lines operated by JR though.

Japan's rails are operated by different companies. So the passes are company/companies specific. It's like RapidKL pass valid only for Prasarana operated trains and buses. Cannot use for KTM.

https://www.jreast.co.jp/multi/en/pass/tokyo_free.html

1 day pass covers almost all the train stations.

But only worth it if you are travelling A LOT.

Tokyo trains n subway not expensive, approx 150-170yen/trip. you need to travel 10 trips in a day to justify buying that pass. I max out at 1100+yen/day when I tour around those places you mentioned.

If only Lake Kawaguchiko area then Fujisan Fujigoko Passport. This passport give you u limited bus ride around Lake Kawaguchiko.

Fuji Hakone Pass on will covered everything in Lake Kawaguchiko, Gotemba , Hakone. Limited Express train from Shinjuku to Hakone Yumoto need pay extra seat reservation fees.

Kawaguchiko area no car rental. You had to rent at Tokyo City and drive to Kawaguchiko. Make sure you you get the ETC package.
Welcome Suica still avalilable for tourist, but it can't be refund the balance credit inside the card.

Yamadaya Hotel checked in time was 3pm. If you reach Kawaguchiko at morning, you can tour around the lake then only go over to hotel. Bus stop just right infront of hotel.

Timetable for "B" Blue Line
http://bus-en.fujikyu.co.jp/pdf/heritageto...time_202304.pdf
13:35 leaving Kawaguchiko Station & reach Shoji Bus Stop at 14:12

If you're iPhone user just add new electronic one to your wallet directly.

Can't. Because E version of Suica are link with Apple pay.

Yes. Make sure you don't top up too much credit inside. It cannot be refund and it only valid for 28 days. By 29th day, the chip inside will self desruction 
erase everything become empty.   

I think its cheaper if u take the local bus pass. There is rental car i think in kawaguchiko

This depends how far can you travel and how much money willing to spend.

Tonight I go back home will update.