Hi,
In that event, a 7 day pass from Hakone would pay off. You don't write if you're returning to Tokyo or not. If not, you can make the trip on the Haruka train to KIX as your last day, then you'd still be able to make the pass valid for a day or two in Tokyo, so you can use it for some of the day trips I already listed above. You can activate your pass at either Odawara Stn or Mishima Stn - the latter puts you about 15 minutes closer to Kyoto.
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are wonderful.
Instead, I highly recommend you make at least half a day open to see Nara either. In Nara, the Todaiji Great Buddha is an extraordinary place, as well as many other historic temples, shrines and gardens in the area.
On another evening, you can also go see Kobe.
You can also use the pass in Hiroshima on the loop bus.
Good luck.