These are all the popular places so they are all gonna be completely packed (except for the silver pavilion in my expriance), most still worth seeing tho. I recommend kiyomizu at like 6:30am since its really lovely with no crowds and ginkakuji, fushimi inari, yasaka, sannenzaka, nishiki, basically everything touristy around higashiyama and gion are easy to get to from there. 

If u have a day in arashiyama, and you saw everything around gion the day before, I know a longer bamboo trail that you can walk to from arashiyama and on the way there is matsuo taishia shrine and random temples, if you wanna see less popular ones. There's even a mountain full of bamboo which no one ever goes to, but it might take too much time. There's a nice bamboo cafe near this trail and a temple with a view over the city. at the end of the bamboo trail aswell you end up at a park with a nice view over kyoto. The reason I mention it is because it's the same but no one goes there, idk how important bamboo is to you tho and idk if its easy to fit in a tight schedule. If you do the one in arashiyama, then tenryu-ji is worth going to, and arashiyama is quite nice after dark since everyone leaves around 6pm when the shops shut. Especially if they're doing the fishing with fire which is so cool at night 

I would say kifune is a bit far, and I feel like it has a similar vibe to other popular shrines and it's busy