What abmj-jr said, with a mention that you'll probably be better off getting a shinkansen and hotel package from somewhere like Sunrise Tours for your Kyoto visit (good value when there are two of you) rather than a JR Pass (which won't be a huge bargain with your planned itinerary)

http://www.jtbgmt.com/sunrisetour/07shinkansen.aspx

The travel company IACE has offices in Japan and the US and can sell you a sunrise tour if you prefer.

You can extend your hotel stay or book more nights independently with this plan.