Well, you have quite a few days looking around Tokyo, including 1 that's open to suggestion. Going this route will probably take a total of 2 1/2 or 3 days. I'd figure 1 day to get to Takayama from Kyoto and see the Hida folk village, 1 day to hike in Kamikochi and then get to Mastumoto, and 1 day to visit Matsumoto castle and get to Tokyo. That's what I did, pretty much (though I went to Kanazawa to see the park there first, and then traveled from Kanazawa to Takayama.) Since you need to be in Hakone on the 3rd to see the festival, I'd do this:
On Oct 28th, skip Koshien stadium and Kobe, instead seeing the museum in the morning in Osaka and then traveling to Kyoto a day early and seeing Kokedera (Saihoji) and Tenryuji that you had planned for the 31st, plus whatever else you have time for.
On Oct 31, Since you arrived in Kyoto a day early, you can now depart a day early, traveling to Takayama in the morning and seeing the Hida Folk village and old town.
Nov 1, take a bus to Kamikochi, hike there during the day, and take another bus in the evening to Matsumoto.
Nov 2, see Matumoto Castle if you like (replacing Nijo Castle, which I think you could skip... Matsumoto Castle is considered 1 of the 3 best in Japan, along with Himeji and Kumamoto Castles), travel to Hakone in the afternoon. If you'd rather skip the castle, you could make it in time to take the ropeline to Lake Ashi that day. If not, you could do it on the afternoon of the 3rd, or on the 4th before going to Tokyo/Yokohama, but that'd mean missing the auto show (was that something you were really interested in seeing?)
Nov 3rd, you're in place to see the festival in Hakone.
On the 4th, you can see Lake Ashi if you haven't yet, or head to Yokohama and see the sights you wanted to see there.
This side trip will take a bit of time, but it's a wild, unspoiled part of Japan that is a stark contrast to the big cities and carefully groomed temple gardens. I think you'd enjoy it! If needed, I'd try and combine some of the Tokyo days to make room for it, but then, I was not a big fan of Tokyo...
More info on Kamikochi:
Kamikochi Travel Guide
Takayama:
Takayama Travel: Old Town
Hida:
Takayama Travel: Hida Folk Village (Hida no Sato)