My favorite thing to do everytime I am in Kyoto is to get up at 4:00 am go on a walk/run. It's great. No one is out on the street except the street cleaners. You get to see the people you rarely ever see---the ones who spend their lives transforming the city for the people who use the city during the day/night. It's like the city is being reborn.
I always go to 7/11 or something and get some sweet unhealthy "pan" (Japanese word for bread, usually has sweet stuff like red bean inside.) and maybe some banana milk if I can find it. If not I usually drink some kind of sesame or red bean drink. These are the things I delight in when I come to Japan.
I love how the sun in Japan shines so brightly, illuminating the neon white sky so early in the morning in summer in Kyoto. It wakes me up instantly, streaming through my white paper curtain, as if nothing could stop its rays.