Wednesday night, after arrival: A Japanese restaurant recommended to us by Kahori, the woman who runs the place we were staying at. Unfortunately I don't know its name, though I could point to it on a map. I don't know if it had a name in English. It had a good variety of Japanese food types and everything was great! My favorite, and one of my favorite dishes from the whole visit, was a simple tomato salad - just tomato slices on greens with dressing and a couple of things on the side. But so good!
Thursday breakfast: We told Kahori we wanted Japanese style breakfast and she directed us to a local set-menu fast food ish breakfast place. Rice with egg, salad with dressing, tofu, tamago, things of that sort. Hadas got the breakfast with natto, but I already knew I didn't want natto so I got one without :)
Thursday lunch: We wanted to get ramen at the place dr_memory and M had recommended, but Fushimi Inari-taisha took a long time and we got to the ramen place in the afternoon to find they take a 3 hour afternoon break. Nearby we found a little local hole in the wall katsu place that was quite excellent. We especially liked some of the appetizers you get for free before your order arrives, including an eggplant thing, and pickled rakkyo.
Thursday dinner: We walked up and down the street of restaurants in Gion near the river, looked at lots of them, and picked a place offering kushikatsu, which turns out to be a Japanese parallel to tapas, with everything served on a stick. Quail eggs, fried chicken, green peppers stuffed with minced meat, salmon with cheese and truffle... amazing stuff.
Friday breakfast: We walked down the main road and picked a place similar to the breakfast places we'd eaten at the day before, but instead of ordering a set menu breakfast we got some of their lunch items. Noodles and katsu curry and side dishes.
Friday lunch: This time we planned appropriately and got to Karako ramen restaurant early enough to eat there. For the first time in my life I got ramen at a restaurant and thought it tasted exactly like what I imagined ramen would taste like. Now I know that feeling of "this is good but not quite what I think it ought to be" that I get at all the places I've tried in the US is not a delusion :)
Friday dinner: Kahori made a reservation for us at a reservation-required sushi place she really likes, Tomi Sushi, and gave us a map and coupon for it. We tried various kinds of fish I'd never seen before at a sushi restaurant. I like bonito, and I can't remember the name of the other one (a bit more unusual) that I really liked. Their toro sushi was amazing! Super soft!
Saturday morning: We had to leave early to get the train to the airport, so we had to eat airport food. Alas.
P.S. I highly recommend Guest Inn Chita if you visit Kyoto. It's a hostel-style inn but you can get private rooms. It's really nice, has a big common room and stocked kitchen, very spacious couples' shower/bathroom, good location, but the best think is Kahori who runs the place. She speaks very good English, is friendly and enthusiastic, and so helpful it's like having a concierge service at a good hotel. When we arrived late the first night and asked for a food recommendation she called the place for us to see if it was still open, and until when. She gave us maps and circled spots on them. As noted above, she made a reservation for us for dinner one night. ... and it's quite cheap!