Best Route on Kyoto Itinerary

I'll reaching Kyoto about noon on 31/Mar, need your help on itinerary below:

Day 1 (Central Kyoto)
Nijo Castle, Nishiki Market, Teramachi Shopping Street, Ponto-Cho @ Night

Day 2 (Eastern Kyoto)
Kiyomizudera, Sanjusangendo, Heian Shrine, Ginkaju (Silver Pavilion), Nanzenji Temple, Path of Philosophy, Gion @ Night

Day 3
Kyoto Imperial Castle, Ohara

Day 4
Arashiyama

Questions:
1. I prefer to walk around and shopping along the way. What is the best route in orderly manner to use for itinerary above as I'm not in a rush?

2. Is it possible to walk around Ohara for half a day?

3. Can I take train till JR Kameoko Station and take Sagano Romantic Train back to Arasiyama?

The itinerary depends on where your hotel is located. So assume your hotel is located around Kyoto Station or Shijo Street.

Day 1:
Nijo Castle first. Then shopping on Nishiki and Teramachi Shopping Streets before evening at Pontocho. Nishiki, Teramachi and Pontocho are all in walking distance to each other.

Day 2:
Sanjusangendo - Kiyomizudera - Heian Shrine - Nanzenji - Walk of Philosophy - Ginkakuji - Gion

Day 3:
Make sure to book the morning tour for the imperial palace, so that you have the whole afternoon for Ohara.

2. Is it possible to walk around Ohara for half a day?

Seeing the main temples (Sanzenin and Jakko-in and a few smaller temples) and seeing the shops along the way can take half a day if you travel at a very slow pace. You could consider a lunch with hot spring at one of the hot spring ryokan in the area.

Can I take train till JR Kameoko Station and take Sagano Romantic Train back to Arasiyama?

Yes. But you have take a bus or taxi from JR Kameoka Stataion to Torokko Kameoka Station. Alternatively, you can walk to the torokko station in about 10 minutes from JR Umahori Station as illustrated here:
http://www.sagano-kanko.co.jp/eng/tram%20access%20route.htm

Hi Uji,

I'm staying just few minutes walk from Kyoto Station.

1. For day 1, how long to walk from Ponto-Cho to Kyoto Station? If take bus, what is the bus number to Kyoto Station?

2. For day 2, Sanjusangendo - Kiyomizudera - Heian Shrine - Nanzenji - Walk of Philosophy - Ginkakuji - Gion. is there any transport needed in between the places? or all within walking distance?

3. is there any shop or restaurant along the road from JR Umahori Station to Torokko Kameoka Station?

4. Is the bus stop at the same bus terminal if I took the bus from Kyoto Station or terminal station Kokusaikaikan Station?

For day 1, how long to walk from Ponto-Cho to Kyoto Station?

30-40 minutes.

If take bus, what is the bus number to Kyoto Station?

17, 205, 5.

A taxi ride costs about 800 yen.

For day 2, Sanjusangendo - Kiyomizudera - Heian Shrine - Nanzenji - Walk of Philosophy - Ginkakuji - Gion. is there any transport needed in between the places? or all within walking distance?

Sanjusangendo to Kiyomizudera is about 20 minutes by walk.

Kiyomizudera to Hein Shrine is about 3 kilometers. An hour of walk. But a lot of it is through the attractive Higashiyama district. Nevertheless, if you do not like walking much, you may want to take a bus from Gion bus stop to Heian Shrine.

is there any shop or restaurant along the road from JR Umahori Station to Torokko Kameoka Station?

I don't think so.

Is the bus stop at the same bus terminal if I took the bus from Kyoto Station or terminal station Kokusaikaikan Station?

I don't understand the question.

Is the bus stop at the same bus terminal if I took the bus from Kyoto Station or terminal station Kokusaikaikan Station?

Thinking about it, I guess you are referring to the bus for Ohara. Yes, both buses stop at the same bus stop in Ohara.

I'll be in Kyoto from 30/Mar to 6/Apr, below are my final itinerary (trip date from 30/Mar - 10/Apr):
day1 (30/Mar) - Nijo Castle,Nishiki Market,Teramachi,Ponto-Cho
day2 (31/Mar) - Nara
day3 (1/Apr) - Himeji & Kobe
day4 (2/Apr) - Kiyomizudera,Heian Shrine,Nanzenji,Walk of Philosophy,Ginkakuji-Gion
day5 (3/Apr) - Arashiyama
day6 (4/Apr) - Morning visit Kyoto Imperial Castle, Afternoon at Ohara
day7 (5/Apr) - Morning at Fushimi Inari Shrine, Afternoon at Kinkakuji (Golden Pavilion)
day8 (6/Apr) - Kyoto Station, Osaka
day9 (7/Apr)- Osaka
day10 (8/Apr)- Osaka
day11 (9/Apr) - Osaka
day12 (10/Apr) - Flight return to SG

Queries:
1. What time is the last bus departed from Ohara to Kyoto Station?

2. Cherry blossom forecast 2008 for Nara at 3/Apr and I plan to go there on 31/Mar. Am I still able to see cherry flowers? Any suggestion date?

3. I plan to go Himeji Castle at 1/Apr, am I able to see cherry flowers on 1/Apr? Any suggestion date?

4. Any suggestion places I should visit for day 7?

5. Any 100yen shop nearby Kyoto Station or nearby area? How I get there?