Kiyomizu Dera - take bus, there is no way you can take train over there
Fushimi Inara - should be hanshin/hankyu line
Arashiyama - keifuku line (randen), or you can cycle over there

there are several passes u can use at kyoto

hankyu tourist pass 2 days
keihan sightseeing pass kyoto-osaka (1 day or 2 days)
keihan sightseeing pass kyoto only (1 day)
kyoto bus only pass
kyoto bus and subway pass
kansai thru pass

do some research on which part u wanna go and relate those passes

icoca can be use at any line in osaka/kyoto/tokyo and works like suica/pasmo

First, do a total daily fare to-and-fro for the places you want to go using prepaid icoca and the Kansai <xxx> pass suggested. I believe your cost will not be higher than daily pass, since you only go 1-2 places a day and not doing amazing race on every stop, hence better to just use icoca/suico/pasmo/etc. prepaid cards.

Hey, tot of just sharing since i just got back from Kyoto / Osaka early this month. I did the whole total costs calculation (estimation thru hyperdia.com) and true enough, ICOCA is cheaper by 5,000 yen.

On the first day arrived in KIX, we took this Yokoso pass where it gave us free subway rides throughout kyoto/osaka for one day, so we save quite a lot for that day. Also took into consideration where would you be staying and whether you would be more on JR or subway as both lines have diff passes if you wish to go for passes.

Since our 3 airbnbs (we moved places) mostly are nearer to subways, ICOCA seems a better fit for us

P.S: If you're a coffee lover, look for % Arabica Coffee at Arashiyama. It's not cheap but the single origin blend is good !