Aussies first visit need itinerey help

Good evening from mainland Europe,

Kobe makes for an absolutely lovely point for arrival, the city has a lot to offer and you will be right in the middle of it when you stay around Sannomiya.

From Kobe I have a couple of places for you to consider, first I would recommend a visit to Hiroshima city. The city has a lot of history and you can make a visit to the iconic Miyajima as well. In addition to making a side trip to Iwakuni which is a small town with a beautiful castle and a bridge which only allowed Samurai to cross during the Edo period.

Leaving Hiroshima, I would suggest Takayama which is a beautiful rural village with a traditional old town. There's also the Hida folk village close by, for those interested in how Japanese lived in previous centuries. The train ride from Hiroshima to Takayama may be a little long but well worth making, the first part is with the bullet train from Hiroshima to Nagoya, where you transfer to the Hida Wideview Express to Takayama. This last part is very beautiful as the train follows the track inward the Japanese mainland mountains, which is home to many scenic sights.

From Takayama you could head for Tokyo or make one more stop at Hakone to enjoy the view of Fuji and explore the beautiful Hakone region before heading for Tokyo.

This way you make good use of the JR Pass and you will visit some of the best places found in Japan.
3 days in Tokyo is a good start, ideally a little more time would be nice as the metropolis has much to offer.

I hope this helps!
Daniel

PS: did you know that greater Tokyo houses more that 150% of the entire population of Australia?