Visit the following websites... tons of info on places to visit and how to get there and also on train schedule. Even suggestions on the travel plans for different sites.
18-135 should be enough for most places and a 50mm lens for low light. A tripod even how basic it is a must. I'm not sure a gorilla can do cos many places will provide you with no perch. You'll be the missing character in any group photo
Dont be too ambitious. Focus on a few places. Nikko, Kakunodate (both north of Tokyo) are great places to make a visit (even as day trip) besides those mentioned above by other CSers. Or take a challenging alpine route in Toyama. All the info and details can be found at the JNTO site. Have fun...