Japan is my favorite place. You could also do a day trip or overnight north to Nara. (it's about an hour on the direct train, but the direct train is not JR (if I'm right), so it's a separate ticket). I love Nara. It's got tons of temples, they are close together and they are stunning. Not a lot of western tourists. I'd recommend an overnight so you can get up early in the morning before everyone gets there. When we were there, it was full of students visiting.

I also recommend the JR pass. We were able to use it on the JR system around Tokyo and so didn't have to buy many subway tickets.

You don't need a guide.