help with planning a trip.

I unexpectedly will be in Japan for 16 days. I was only suppose to be going for a few days. I am excited, but now I need help planning on what to do. I got a 7 day rail pass, and I would like to use that as much as possible, and perhaps stay in Kyoto for part of the trip. I want to for sure go to Kyoto, Hiroshima, and Tokyo, but other than that I am open. I like shrines and temples, and also running brooks/nature. I also like going to lesser traveled places. Am I able to take my luggage with me on the train? Also, I do not speak Japanese so I am not sure if that will be a problem. Thanks in advance for any suggestions!

If you like forests and things, could I suggest something along the lines that, after you have visited Kyoto and Hiroshima, you go back to Tokyo by going Kyoto - Kanazawa (train) maybe a night in Kanazawa, then bus or train to Takayama (stop by Shirakawa if you are going by bus, stay at least a night in Takayama), then bus from Takayama to Kamikouchi (stay at least a night in Kamikouchi) then bus/train to Matsumoto (visit the castle) then train to Karuizawa via Nagano (about 2 hours, stay the night at Karuizawa or maybe 2!) then back to Tokyo. That'd be a pretty easy trip, even for a lazy guy like me.