that you can see before you say you're done seeing shrines, etc. I did a Japanese mission, so I know my way around a little better, but it just takes a little time to figure it all out. If you're wanting to take a bullet train to Kyoto, get the JR pass for the week... there's another pass that'll allow to go to Sendai (a 2+ hour ride each way. I went up, looked around and came back) and Niigata that's a little cheaper than the full JR pass. I think it's call a JR East pass.
What to eat? LOTS of gyudon, katsudon and noodles.. both ramen and all sorts of udon and other noodles. Very palatable to the american mouth.
My son and I did Tokyo Disney for one of the days we were there 2 yrs ago. There's Disney Sea (like World or Land) and the usual park. It's nearer Narita airport, so we did that the last full day and then headed to the airport