Hi there,
That's a lot to include in a single day. I think I would start in Arashiyama, travel to Kinkaku-ji - Nishiki market and then head to Tofukuji and Fushimi Inari. Kyoto is very much a bus city, so learning the bus system can be a great help to get around. Here is a full map. If you stay close to Kyoto station, then you can use the JR for travel to Arashiyama, Tofukuji and Fushimi Inari but there are no JR lines near the other palces.
Also consider taking a taxi from time to time, prices are not that high for travel within Kyoto city, especially if you share it among multiple travelers. This way you spend more time seeing what you like and less time traveling.
Hope this helps,
Daniel