I'm likely going in November as well so I've been looking up where to go. These aren't in Tokyo but maybe worth the visit. Omori Factory in Yokohama has to be worth a visit (Nismo factory). There's also Toyota MegaWeb in Odaiba (which is in Tokyo!), Mazda are in Hiroshima etc. I looked at this for a few ideas:
http://www.7tune.com/japanese-car-mu...t-you-started/
MegaWeb is more of a theme park apparently but there's also a History Garage with loads of old road and racing cars.
Outside of that, Akihabara for any nerdy/anime/tech, Tokyo Skytree, Tokyo Tower. Senso-ji temple (in Asakusa, Tokyo) is probably worth checking out if you're interested in the traditional side. I'm still trying to work out where I'll have time to visit!