There are different ways to go about Hakone.
(1) start early from Tokyo, and do the round course back to Hakone Yumoto on the first day, stay in Hakone Yumoto, then on the second day get back to Odawara, then take Shinkansen to Kyoto from there,
OR,
(2) you can start a bit late from Tokyo, then stay at a hotel/ryokan *halfway* on the Hakone round course, meaning some places like Gora, or on
the lake (Togendai), or in Moto Hakone, then the next day take the bus down to Mishima station, and continue to Kyoto from there.
OR
(3) you can simply go to the ryokan in Hakone Yumoto in the late afternoon, just for enjoying the hot spring and dinner there, then you can start off in the morning of the second day to do the round course, taking the bus down to Mishima to continue to Kyoto.
Hotel area suggestion if you want to stay somewhere *halfway* on the round
course:
http://www.japan-guide.com/forum/quereadisplay.html?0+6...Seeing that you'd have arrived in Tokyo only on the day before, you *might* be tired or want to see Tokyo more, so one option would be to travel around Tokyo in the morning, then travel to Hakone in the late afternoon; this one is your thread, right? :)
http://www.japan-guide.com/forum/quereadisplay.html?0+6...Some suggested travel from Hakone to Kyoto:
http://www.japan-guide.com/forum/quereadisplay.html?0+5...In any case,
1. the ryokan looks nice;
2. You enjoy the onsen AT the ryokan :)
3. 4. If you have activated your JR Pass when you start your trip to Hakone, then take JR Shinkansen to Odawara, and buy Hakone Free Pass there. From Odawara, you take the Hakone Tozan Line to get to Hakone Yumoto station.
5. At Odawara. They only come in 2 or 3 days.
