There's probably a good solid 3 nights/4 days worth there and if I were you I'd bookend it with maybe a trip down to Hiroshima - genuinely about 2 hours by bullet - which should not be missed.
So very bold to consider going for such a short period of time as Japan is a seductive soul that will entice you by everyone of your five senses....
I can't add anything to the ideas already quoted above but suffice to say the only consideration for me would be can we wait until we can fit in...