[samurai007]

Just a note: The train from Osaka to Koya-san is not a JR train, it's a Nankai train, so you can't use your JR pass on it. No point in activating the pass until after you get back to Osaka. In fact, it seems like you won't really get much use out of the pass at all... the only day you'll actually save money is the day yo go to Tokyo. You might consider skipping the pass altogether and taking a night train to Tokyo, or some other cheaper method than the bullet train.