3 days Kyoto on 16 Nov 2012

I would like to visit the following places in Kyoto and Nara in 3 days but very confused in arranging the route.
Arashiyama, Kinkakuji Temple, Nishiki Food Market, Kyoto Imperial Palace , Toji Flea market,Gion, Pontocho ,Philosopher's Path
Nijo Castle, Tofukuji Temple, Fushimi Inari Shrine. Appreciate if someone can help to plan the route for me as I arriving in Osaka on Fri morning. I am thinking of getting the Kansai thru pass as Im going for 1 day trip to Kobe Arima too. Thks.

The Toji Flea Market ison the 21st, so you cannot visit it.

Kyoto Imperial Palace requires advance reservations. If you have not already made them online, you will have to visit the office in the Kyoto Imperial Park and make reservations in person. The palace is closed on Sunday.

I recommend to avoid Tofukuji on the weekend because it will likely be very crowded. Visits in the early morning are usually quite pleasant.

I recommend to group the sites into groups geographically and create day plans accordingly, considering the above mentioned constraints.

North:
Arashiyama
Kinkakuji Temple

Central:
Nishiki Food Market
Gion
Pontocho
Nijo Castle
Kyoto Imperial Palace

West:
Philosopher's Path

South:
Tofukuji Temple
Fushimi Inari Shrine

The time to visit the above places varies drastically between individual travelers and how much they want to see. Generally speaking, single sites usually require about one hour, but districts like Arashiyama can take anything from a couple of hours to an entire day depending on pace and interest.