Hi there!
Travel around Kyoto is fairly easy, even if you travel with a disabled individual. The best way to travel around Kyoto is by bus and over 80% of buses in Kyoto are equipped with wheelchair access and priority seats for elderly and persons would would otherwise need them. When you travel by bus consider buying a 500yen bus ticket. Which allows for unlimited travel on buses in the city.
The first part from Kinkakuji to Arashiyama can be a little tricky, you can take a taxi from Kinkaku-ji to Enmachi and then the train to Saga Arashiyama. A better option may be to take a taxi to Kitano-Hakubaicho and from there take the Keifuku line to Arashiyama. This train ride is very scenic and will get you closer to Arashiyama than if you take the JR from Enmachi.
Day 2.)
a.) Travel to Kyoto station by bus, At Kyoto station take the Nara line and get out at Fushimi Inari.
b.) Return to Kyoto station and from there take the Karasuma Subway to Shijo Station, it's about 5min walk from here to Nishiki market.
c.)Kiyamachi and Pontocho are walkable distance from Nishiki Market, simply head to the Kamo river (Kamogawa) Kiyamachi and Pontocho are parrelel to the river.
Day 3.) There are several buses going to Kiyomisu-dera, I don't know the exact numbers so I would recommend asking the staff at your accommodation for the best way to get there, it's not too far away so you could also consider taking a Taxi.
2.) You can take bus nr 100 directly from Kyomizu-dera (Kyomizu-michi bus stop) to Ginkakuji.
3.) You can take bus nr 100 going back to Kyomizu-dera and get out at Gion. Gion is quite large, so I would recommend taking a taxi back to your hotel, as it is not very far away.
Also see this BUS MAP which all city bus routes in Kyoto to make your travel easier.
I hope this helps you!
Daniel
