I'd advise against getting the JR pass. Suica/ICOCA is sufficient in my opinion to go round Tokyo/Kansai. My 10 days in Kyoto/Osaka cost about 15k yen ICOCA credit. I blame myself for taking the bus for 2-3km ride  . Not to mention getting on the wrong bus so many times.
Just proved more to my AirBnB landlady Malaysians are lazy on our feet.

Shinkansen costs 13900yen(Hikari reserved) from Tokyo to Kyoto.. Osaka tho a little bit more around 14500 yen perhaps. Not sure since I rode from Tokyo to Kyoto 
Then again, if you are taking 2 way ticket, its the same price as a 7-day pass.

Personally I won't take night bus since most definitely I will not be able to sleep, or will be tired from journey.
But I do know people who can sleep soundly with a snap of a finger.

i realized you guys only mentioned number of cities to be visited...but no mention of how many days ?

have u been to japan before? if nope then i strongly suggest u either go tokyo 10 days or kansai area 10 days. by covering two regions u will be quite rush and might not cover everything as well.

have u already make some rough itinerary? i can help u fixed it a bit if u do. coz im not sure 4 days can cover so many things in tokyo especially u got quite a few places tht requires half a day minimum

itinerary of the places like 1st day asakusa, tokyo tower, and so on

Ah that must be the famous restaurant in Dotonburi. I got the boiled, raw, grilled crab, kani suki, porridge, pickled veg and fruit set.
To me it is very nice. Pricey tho..

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Accurate enough. I recall the sets starts from about 4k up to 16k i think? Of course, the lower price wont land you the good stuff. Don't quote me on that 
That set in pic is uh.. 11k I believe with tax. It depends on which set you choose.

I started with boiled crabs, then they presented raw and grilled crabs.
Then comes nabe withe veg and more raw crabs.
I was almost done, so I just sit back with my drink and JUMP. All of the sudden, they came and prep the almost drained broth to make porridge. I totally forgot about the porridge. Its sooooo good.
They'll let you determine how thick you want it to be. Me being a noobie just tell em 'hai, hai, ii desu, daijoibu desu' all the way.
Dinner ended with fruits...and ice cream? cant remember that..

LOL after you checked how much it costs to get from one place to another till you arrive in Kobe without usage of pass.