Finally going to Tokyo!

Yest at Marina Square CTC travel fair, was checking out Tokyo free & easy $600 plus for i think 3D2N? But after all the 'hidden costs' plus 1 night's extension, it ended up as $1.3k plus per pax for 4D3N for flight & accomm. They said jap hotels usually dun offer breakfast daily. It's alright, we can venture out and explore...

Initially wanted to go Melbourne, but ALL FLIGHTS FULLY BOOKED in the period of Sep- Hari Raya holiday that week. 

But nevermind, going Tokyo seems more exciting :)

Has anyone gone before? Any recommendations on where to eat, where to go (they told me Shinjuku, and some Taka got blue label-but not sure if getting (how much issit i wonder?), some other place got bookstore). So any info on where are the Must-Go, Must-Eats, Must-Sees will be greatly appreciated.

Also wondering if where in Tokyo serves Kobe beef? And lastly, initially wanted to book Onsen package which will end up $1k more, but in the end, heard it's gals and guys separate, then it's a bit weird to be stark naked in front of strangers. Anyone knows of any onsen that's for couples? Where is it? Can just 'rent onsen' or must book room then can?