If you're taking the Shinkansen at least twice (assuming you arrive in Tokyo and depart from Tokyo), then it will be worth it. For the convenience and the cost as well. The slowest Hikari bullet train will set you back about RM480 one way 180 mins. Nozomi which is the fastest at 150 mins, is about RM40 more and it saves you only 30 mins. Add the fact that you can use it on JR lines and buses, it may save you a lil bit of money and added value of convenience.

JR Pass at current exchange rate is about just under RM900. So, if you're only flying in Tokyo and departing from Osaka, then it's probably not worth it since you're only taking the bullet train once.

Pasmo cards only works on metros/subways and saves you about 5 Yen per trip. The rail looks complex but you'll get the hang of it after several purchases. The complexity of it is when looking for the correct line to take, especially at the bigger stations like Shibuya/Shinjuku.

My third trip is coming in November. BANZAIIIIIII ....

Indeed, thanks for the correction