I tried to respond to your PM but you have not enabled an e-mail address to receive them. I wanted to point out that I had added some new info to my original post and you might want to skim through it again to pick up the additions.

Looking at your admended first post, I only see one potential problem. You have scheduled major train travel on 8 days, 9 if you count Hakone-Tokyo. That is not a problem if you are paying out-of-pocket for trains but is a problem if you will be using the 7-day Japan Rail Pass. With the distances you have planned, the Pass would save a lot of money.

I don't think Hakone is worth a day but others do. YMMV.

JR