We went to Japan for our honeymoon too!
Jigokudani Park (monkeys in hot springs) was a real highlight for us. Not sure if October is a good time but if it is I'd recommend checking it out!
Lots of other good recommendations here. For Tokyo....Harajuku was everything crazy you expect from Tokyo.
Golden Gai is worth checking out for an evening - a bunch of tiny 4-6 person bars all crammed in one street.
Everything is cash based in Japan so make sure you take lots of Yen. That said, it's very safe so you need to be concerned about carry thousands of yen around.