Japan is an amazing place, Kyoto for me was one of the best places to go, yes... after a while the Temples do start to mold together. However, if you walk about and try to head to the outskirts you will find far far far better places/temples then the tourist trap ones in the centre. We took a bike ride up the river, took the right hook further north and eventually came off and went north on some roads. Out of nowhere we saw these steps leading into a forest and decided to walk up and see where it went. Wow, we found the most sublime, quietest, tranquil temple/monk house we've ever seen and not a tourist/drink machine anywhere near.
Also everyone was helpful in Kyoto, where as in Tokyo we saw a lot of underage prostitution and a lot of bad attitude from people rushing around. But there is so much to see in each city, but also take it steady and just enjoy it as much as you can.
Food wise, I found shop ready made meals/ meats to be overly salty. Resteraunts were fantastic though and a lot of places have images/ready made choices on show. If you are in kyoto, head to Shijo Dori and look out for BENTO 250 sign looks like a small cupboard shop, right infront of a hotel with a bear image on it's side and opposite a 7/11. Bit salty on occassion but some of the meals in there were tasty! and at 250 yen, cheap but well worth it.
Night out wise in Kyoto, Head to near the Gaisha district for some of the better / touristy bars and if you like rock (especially jimmy hendrix) head to One in Kamiyacho. It's a small pub on the second floor of what looks like small apartments but the barman in there is/was/will always be my favourite person in Japan, fantastic bloke. Also many bars around here, at the weekends especially, will have tour guides on there time off so I'd suggest talk to a few and get some tips/ideas from them like we did and we found some rare moments that we will always cherish because of their information.
Take a few small English gifts to give to people if you like them, this is one of the greatest signs of respect and friendship (from my experience) that they have. I gave one guy a simple flag on a pole (tiny £0.99 cost) and he got so happy and joyous he invited us around the next evening for a meal with his family and bought us several drinks that night. Because of this I met a great family who still keeps in contact and on our next visit over there wish to see us again, and possibly stay with them for a couple of nights.