bus

1.have jr pass. how do we get from kyoto station to fushimi inari shrine.
2.then fushimi shrine to kiyomizudera temple by bus and/or jr line.
3.then kiyomizudera to nishiki
food market by bus. 4.then nishiki to kyoto station by bus

have jr pass. how do we get from kyoto station to fushimi inari shrine.

A 5 minute ride by JR Nara Line:
http://www.japan-guide.com/e/e3915.html

then fushimi shrine to kiyomizudera temple by bus and/or jr line.

The easiest would probably be to return by JR to Kyoto station and take the bus from there. The following bus network map lets you look up the routes:
http://www.city.kyoto.lg.jp/kotsu/cmsfiles/contents/000...

If you're going to use the bus much, don't forget to get a day pass at Kyoto station. An unlimited ride all-day bus pass is just 500 yen (a single bus ride is usually 220), and an unlimited bus and rail pass is 1200 yen, but when I went we didn't use rail at all. The bus network is plenty extensive

Oh, it's worth mentioning that the 500 yen passes are sold in these vending machines outside at the bus terminals, not at the visitor info counter. I only saw them selling the 1200 yen pass