Wonderful transport system in Japan

Japan inter-city transport expenses:
Japan Rail pass (7 days) - ￥28,300 (approximately RM1,020)
Pasmo prepaid card - ￥5,000 (around Tokyo plus return train to and from airport without JR pass) I think this can be lesser if I studied the train map and plan thoroughly but well didn't really want to strain my brain during holiday. I did alot of hop in/out and transfer from one train to another with pasmo, some were due to lost
Kyoto - Bus to Gion ￥220 + ￥500 unlimited bus day pass (must buy cos it a super value)
Kyoto -  Subway 500 to Fushimi and bus ￥220 back to Gion from Kyoto station. This I should have use JR pass to get to Fushimi and Arashiyama from Gion-Shijo station.
Kyoto to Osaka - Gion to Kyoto station, this too should use JR pass from Gion-Shijo station to Kyoto station.
Later finally within Osaka I manage to cover all with JR pass.
Osaka to Takayama by JR pass, return bus ticket to and from Shirakawa-go ￥4,300.
Takayama to Tokyo by JR pass.
Day trip to Nikko - World heritage bus to the touristy spot around Nikko￥560
Total expenses used outside of JR pass ￥11,300

Grand total used in transport - ￥39,600 (approximately RM1,400)

Car 16 of the Shinkansen Hikari 503 bound for Shin-Osaka

Shinkansen moving in/out the station rapidly

in the green car seat

you can hop in/out anytime any station with JR pass, without reservation, just refer to these board at the train platform and take note of the non reserved car number to wait at queue. Shinkansen can run out of seat too, especially during their peak hours on weekdays and I think all the time during weekdays.

Shinkansen from Nagano to Tokyo (transit from Takayama limited express) one may see Mount Fuji by sitting on the right hand side of the train. This is a super busy destination so suggest to book a seat a day in advance at the JR ticketing office.

JR monorail which stops at Fushimi @ Kyoto

Heritage bus @ Nikko - be sure to check out the package pass, it can be pricey if you hop in/out from spot to spot

JR monorail to Nikko

I would described Japan transport system with 2 words - timely and systematic. Folks in  KL that has problem keeping up with punctuality will have a big issue if they were posted to Japan.