I lived in Kyoto for 6 years, so I will give you some advices.
(But I cannot speak English well because I'm Japanese, sorry.)
Your plan has many waste time,
Gion, Kiyomizudera, Ginkakuji + philosopher path : Eastern Side in Kyoto
Sanjusangendo : South Eastern Side
Kinkakuji : North Western Side
Arashiyama : Western Side
Nishiki market : Central of Kyoto
Fushimi Inari : South Side
so, you should change your plan.
If you want to see Eastern Side, philosopher path is main.
That path's north end is Ginkakuji, and it passes Nanzenji, Heian shrine,
Yasaka shrine (in Gion), south end is Kiyomizudera.
Southern half of way is very difficult to get your way in first time.
But it is 10 km from Ginkakuji to Kiyomizudera, and many people walk,
Cheer Up!
Fushimi and 33gendo are on the way to Kyoto from Osaka, if you use Keihan Railway.
JR is not useful for Kyoto trip, because it has less stops
than other train or bus, and it costs more.
Arashiyama and Kinkakuji are near, but no bus connect each other.
so, I think better
Morning : Kinkaku or Arashiyama
Noon : Nishiki market
Afternoon : Arashiyama or Kinkaku
In Nishiki market in 26-31/12, many Japanese will come to shopping for
their preparation for New Year, so a lot of traditional things (most is food)
are in the market.
At last, about ticket.
In kyoto city, many ''company'''s buses run, and you can use Kyoto 1 day buses pass
only for Kyoto City Bus.
Please use map about Kyoto City Bus:
http://www.city.kyoto.lg.jp/kotsu/cmsfiles/contents/0000019/...PS.
When you go to Arashiyama, Please eat Yudoufu(Boiled toufu)!
walk 150 meters for north from Arashiyama Station of Keifuku Railway,
there is very small street stand of Yudoufu, and I think that shop is the most
delicious of Yudoufu.
And on the philosopher path, there is a cosmetic shop ''Yo-jiya'', you also see it.
Kyoto has many Yo-jiya shops, but that shop has very beautiful gurden.