Was in Japan last year with our 2 year old
Didn't actually find it very expensive - the exchange rate was good and we live in london and it's deffo not as expensive in comparison!
We didn't do as much as we would have liked as had the toddler with us so slowed us a bit
But rough itinerary was
3 days Tokyo
2 days Disneyland
5 days Kyoto / Osaka / Nara (stayed in a lovely Ryokan in Kyoto as the base and it was amazing and easy to get to Osaka and Nara from there!)
back to Tokyo for 5 more days!
We did some day trips - one was a hello kitty bullet train from Osaka to Hiroshima
Eating out we tended to stick to family style places becasue again toddler - and needed space (I did go to some little Raman bars alone and stuff super affordable!)
MY daughter LOVED the conveyer belt restaurants so we went there a few times
Got lunches / snacks on the go sometimes in 7/11
Coffees from the vending machines
Rail pass is a must
Just had a quick look at spreadsheet we had - and we only spent 1700£ on accommodation!
Rail pass was £452.82 (we only got a 1 week one as it was all we needed! but 2 weeks would be good if you think you'd travel more!)
We use a BA amex for all spending and had a companion voucher so flew premium economy and we paid £1097for flights!
So all in was around £3500
We are going back next year to do more of the Country it was just amazing