I always use a sun cream SPF 50 PA+++. And many Japanese girls use a sunshade as well. Perhaps it may sound old-fashioned, but don’t hesitate. It’s not out here.
There are various cute sunshades, also folding ones, which you can find around 1500 yen.
I suppose jeans will be fine, I myself wear jeans also in mid-summer actually, but it depends on what you're planning to do.
A few years ago I went to Kyoto in a sundress with mid-heel sandals. That was okay for me, though I recommend you to pack the clothes in which you feel comfortable.
And the shoes, too, for you probably go through gravel paths in Kyoto.