you taking first (non-Nozomi) shinkansen using JR Pass?
Else, first (Nozomi) shinkansen departs Tokyo at 5.37am and reaches Kyoto at 8.05am.
HyperDia | SearchResult
10.30am a bit late to go to all those places. even if you take cab in between the places in eastern kyoto also quite rushed i think.
usually eastern kyoto alone can take up one whole day, especially since you thinking of going to both kiyomizu and ginkaku which are at different ends, not forgetting the earlier closing times in winter.
day 2 is more manageable, if not enough time, maybe can drop nijo castle.
i will get the bus pass for both days for the convenience even if i'm only making 2 trips, since it's only 60 yen difference.
day 3, are you rushing back to Tokyo to catch a flight? otherwise, i suggest you can drop by fushimi inari quickly. it's just 5 mins from kyoto station. if you don't plan to hike up that far up the tori gates, i think 30 mins can be done.