On the difference between Kyoto and Tokyo, I guess it comes down to size. Tokyo is the largest city in the world, and it feels like that when you're there. There are a ton of people, a ton of places to eat, a ton of places to shop, and a ton of things to see. But beyond that, it's also a city of contrasts. You can be in an ancient temple one minute and feel like you're in the future the next. You can wander around the Imperial Palace grounds, parts of which are nearly deserted, and then go down the street and be in Tokyo Station, which will be packed.
Kyoto is much smaller. The buildings are capped at (I think) ten stories. There are a thousand temples and shrines, allowing more time for quiet and reflective sightseeing. And as you walk along through the Gion, it's just a very pretty city.
On the bento box, I don't have any real suggestions. At the station, there are a bunch of different shops that will be selling snacks. You can just peer around and see what strikes your fancy. Even if you're running late, there's always a little shop on the platform that is going to have a decent selection of bento boxes and beers.
That's honestly the bit about Japan that takes the least planning or thought.