[kenmei]

I've just got a few comments to add:

first, you have an amazing trip planned...extremely busy one, but amazing. i'd only be worried about getting tired and wanting to take a little time off to rest. but for sure, you'll be getting your money's worth with the JR pass.

speaking of the JR pass, like MMM said, JR pass is for JR trains only. In Osaka I rode the subway, and tried to pass thru with my JR pass but the clerk at the counter said "no no". I didn't even realize it wasn't a non-JR train! Haha, just pay attention, more than I did...but you shouldn't have much of a problem. Anything local by subway isn't too expensive, if you have to go that route.

thirdly, about Hakone. please please please, book a hotel/ryokan that has an Onsen! It's an amazing experience and every foreigner should try it! (it being hot springs).

I'm amazed at how much you want to do and how you want to see of a more "traditional" Japan. Good luck and enjoy your time. Don't be shy to ask Japanese for advise, they're really friendly.