14 day trip in Feb.- Himeji-Kyoto-Tokyo

This will be my first time visiting Japan and I was wondering what the most efficient way (financially) to pull off transportation. Our current itinerary is:
Himeji - Two days
Kyoto - Six days
Tokyo - Six days

I was initially going to get a rail pass, but I think that will end up more expensive in the end.
Any advice anyone has to offer is appreciated!

You are not going to enter Japan through Himeji, are you? If not, note that it will be relevant to your question whether you are entering though Narita Airport, Kansai Airport or some other airport or port.

The cheapest way to travel are likely night buses for the long distance trips:
http://www.japan-guide.com/e/e2366.html

Here is a good suggested itinerary.
http://www.japan-guide.com/e/e2400_osaka_12.html

Oh! sorry! We're planning of flying into Kansai then busing taking a train to Himeji. Just to clarify. :)

So... To add more detail as to what's going on:
We land near Osaka and bus to Himeji.
Two days later, we see a rock concert. Head out to Kyoto the following morning.
Wander Kyoto to my heart's content for 6 days.
Bus it to Tokyo and do the same for 6 days.
Go to Narita and I'm done!

I wanted to purchase a 4-day Kyoto pass, then a 7-day Tokyo pass, assuming that the train is the most efficient way to go.
I had heard somewhere that many of the bus lines around Kyoto are not JR, so the passes won't work. Is this true?
Thank you so much for your time and assistance.

The bus from Kansai Airport to Himeji costs 3000 yen. With a 1-day JR West Kansai Pass, you could make the journey by JR trains for 2000 yen:
http://www.japan-guide.com/e/e2361_03.html

Kyoto to Tokyo is most financially effective by night bus, as it is not only one of the cheapest ways to travel, but also saves you a night of accommodation cost:
http://www.japan-guide.com/e/e2363.html

2 days seems a long time to spend in Himeji, itfs not a very big place. I did a day trip there from Osaka and it was enough time to see Himeji castle and wander around.

I wouldnft get a JR pass. I would get a 3 or 4 day JR west Kansai pass (I think that is what you meant anyway). It is 5000 for 3 days and 6000 for 4 days. It will get you from the airport to Himeji and then from Himeji to Kyoto using the JR trains.

In Kyoto most of the tourist places are accessed using the buses. You canft use JR passes on these buses. The best option is an all day bus pass for 500 yen.

The train from Kyoto to Tokyo is 13 500 yen for the Nozomi train (fastest trains that JR pass canft be used on). There is also a special where if you buy your Kyoto to Tokyo train ticket 7 days or more in advance it is 12 000 yen for the trip on a Hikari train (second fastest train).

So given these prices I think it is cheaper not to get a JR pass for your trip.

With 6 days in Kyoto it would be a shame not to see Nara and Osaka for 1 day each. As another poster said, Himeji can be easily done in one day. I also assume that when in Tokyo you will go to Kamakura and Yokohama? if only because Tokyo, having being destroyed twice in the 20th century, doesn't have much historical buildings. As for big department stores, Osaka and Kyoto have them too (some of the same chains too)