You should use Arukumachikyoto for planning.http://www.arukumachikyoto.jp/index.php?lang=en
I recommend the transportation methods in the following order: Walk, Train, Taxi then Bus. You should take bus sparingly. Avoid if possible bus afternoon and in the “central area”.
You will have 5 days so you can concentrate one region per day. Below is a sample itinerary.
Day 1 Higashiyama district south
Kyoto (JR) to Inari (JR) by JR train 5 min, 140 yen. Fushimiinari shrine
Fushimiinari to Kiyomizugojo by Keihan line 5 min, 210 yen.
Walk from Kiyomizugojo to Kiyomizudera (20 min)
Kiyomizudera to Kodaiji then Maruyama Park, Chion-in and Shoren-in.
Higashiyama to Kyoto by subway 15 min, 260 yen
Total 610 yen (JR, Keihan and subway)
Day 2 Higashiyama district north
Kyoto to Keage by subway 17 min, 260 yen. Nanzenji, Eikando, Heian shrine, Murinan, Honenin, Ginkakuji.
Ginkakuji to Kyoto via Marutamachi by bus and subway, 41 min, 490 yen
Total 750 yen (Subway 520 yen and bus 230 yen)
Day 3. Central Kyoto and Kinkakuji
Kyoto to Nijojomae by subway 20 min, 260 yen. Nijojo
Nijojomae to Kinkakujimichi by bus 23 min, 230 yen Kinkakuji
Kinkakujimichi to Kyoto via Kitaoji by bus and subway 34 min, 490 yen
Total 990 yen (subway 520 yen, bus 460 yen)
Day 4. Arashiyama
Kyoto to Sagaarashiyama by JR 17 min 240 yen. Arashiyama
Sagaarashiyama to Kyoto by JR 17 min 240 yen.
Total 480 yen.
Day 5. Ohara
Kyoto to Ohara via Kokusaikaikan by subway and bus (Kyoto bus) 48 min 640 yen. Ohara
Ohara to Kyoto via Kokusaikaikan by subway and bus (Kyoto bus) 48 min 640 yen.
Total 1280 yen (subway 580 yen, Kyoto bus 700 yen)