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if you want to see some amazing temples and you get the chance I suggest going to Kamakura its 45 mins on the train from tokyo station

there's some beutifull zen temples and the great bronze buddha of course and you can see the whole area in less than a day because its not particually big

also its on the shore so you can see the beach and everything

plus its where elfen lied is set cant think of any reason you wouldn't want to go :P

edit
also just rembered I didn't bother with the japan rail pass I waited till I got there and got the suica & N'EX pass which I found much more usefull and a little cheaper Im not sure if it will be cheaper if your traveling all over japan but always good to have a few options to compare ^_^