Japan Trip

I will be traveling to Japan with a companion in March for about 10 days.
The problem is trying to figure out what to do.

We'll be flying into Tokyo, but I'd also like to visit Kyoto and maybe a few other cities.
What is the best way to get there for the cheapest amount? Is it worth getting a JRail Pass?
Where are some interesting places to stay?
Also, what are some sites that are worth seeing?

Thank you for your suggestions!! =]

The problem is trying to figure out what to do.

I recommend to get an idea of what there is to see by reading guide books and a website like the following:
http://www.japan-guide.com/e/e623a.html

What is the best way to get there for the cheapest amount?

It depends on your exact itinerary!

Definitely get a JR pass if you are travelling between cities and villages. We had a 14 day holiday in Japan last April, staying in each place one, two or three nights. The pass would have saved us bucketloads in money and time.

For your reference, here is a stardard and excellent suggested itinerary.
http://www.japan-guide.com/e/e2400_tokyo_8.html

If you make a return trip between Tokyo and Kyoto/Osaka within 7days, 7 day JR Pass pays off.
If you fly into Tokyo and take off from Osaka, it is advisable to get SUICA prepaid card and use it in Tokyo, Kyoto and around Kyoto.