I’m planning on heading out Toyko in August or September of this year. Still in the saving process as well. I’ve been looking at tour groups recently, as there are quite a few places that will do full tours of Tokyo for a few days, then full tours of Kyoto for a few days. The rail pass and some meals are generally included. Since you have friends that you would be staying with, I would see if they would be willing to take you around and really get immersed in the culture, the stuff real people do, not what the travel companies want to show you.

As for cheap airfare, I’ve setup some price alerts on Kayak.com, when tickets hit the price point I want, I will get an email letting me know rates are where I want them to be. Defintiely check out that site. I would also do a quick Google search to see when the cheapest days to buy tickets are (yup, apparently some days are cheaper than others).

Good luck with your trip! I hope you make it over sooner, rather than later!