how many days in Kyoto

We're going to Japan for three weeks in November and we are trying to work out our route. Would three full days in Kyoto be enough to see the sites.
we'd like to then spend a night in Nara and a Night in a temple in mount Koya

It depends on how much time you have in Japan and your interest in Kyoto as opposed to other destinations.

For example, if you are in Japan for just four days and are not very interested in historical Japan, three days for Kyoto is probably too long. But if you are in Japan for two months and Kyoto has been your dream destination for years, I would recommend to spend more time in Kyoto.

For the average traveler, I think that three days is a reasonable amount of time to spend in Kyoto. It will be enough to see several of Kyoto's major sights.

You'll be in Japan when the maple leaves turn color. Kyoto's temples and shrines can be spectacular at this time of year. I would stay in Kyoto a week and use it as a base for day trips to Osaka, Nara, Kanazawa, etc. besides seeing the sights of Kyoto.

http://www.japan-guide.com/e/e2014.html

Just to give you an idea it is said that there are 1600 temples and shrines in Kyoto..plus a few palaces,lots of gardens, lots of interesting stores from huge to tiny.. then there is Nara, with at least several dozen historical sites, and other towns in the Kansai close to Kyoto, like Kobe, Osaka, Himeji etc. etc., each one with interesting sights of all kinds.