Agree with jib-san. In the morning, just check out of the hotel, take a cab or local transportation to Shinagawa Station and trade your exchange order for the Rail Pass at the JR office there. At the same time, they will make your seat reservation for the next shinkansen to Kyoto.

Don't forget about the occasional cab when time is important. They are safe, reliable and not too expensive if you limit their use to times you really need to get someplace quickly with no hassle.

In Kyoto, you can purchase a prepaid bus/subway combination pass at the bus office just outside the Karasuma entrance of Kyoto Station, just to the right of the bus queues. They come in 1,000 and 3,000 yen denominations. The 1k yen version has 1k yen value. The 3k yen version actually gives you a bit of a discount, 3,300 yen worth of rides for 3,000 yen. Just slide the card into the slot to enter a subway platform and as you exit. Most buses have a slot at the front, near the driver where you slide the card as you exit. From Kyoto Station, you will find that routes 100 and 101 are most convenient for tourist spots.

Before you exit Kyoto Station, I recommend a visit to the Tourist Information Center on the 9th floor. Just take the escalator up to the top, turn left and follow the signs. They speak English, have maps and other information and public access computers (100 yen/15 minutes) for emailing home and such.