re: Headed to Japan in April...

In Kyoto:

Ryoan-ji right when it opens
Fushimi-inari at sunset. It can be a hike to the top. We got to the top only to find it wasn't the top and there was still more to go.
Hike up to the temple at the top of Mt Kurama and then hike back down the other side of the mountain through Kibune
Eat weird shite at Nishiki Market
Nighttime bar hoping along Kiyamachi Dori
The sake district sounds good on paper, but meh, not the best.

We had an AirBnB just west of the Kiyomizu subway station. It made for a pretty decent central location. There wasn't really anything directly by it besides a cool bar and ramen place, but we were a quick train or bus from everything else.