Thanks for the help. I'm looking into the Seishun ticket and it seems like a good deal. The only problem is that they're effective from July 20 - Sept. 10 during the summer and I most likely won't be in Japan during these dates. I should be able to catch the Seishun deal if I go during the winter.
I still haven't bought plane tickets but will most likely go before this time since prices seem cheaper. How bad is the rainy season in Japan? Bad enough so that you're stuck indoors most of the time unless you want to constantly be under an umbrella and can't take any pictures without getting your camera wet?
So you can use those 5 days with the Seishun ticket whenever you want unlike the JR Rail Pass which expires within 7 consecutive days after first use? If so, I guess it's most wise to use it for long distances to really get your money's worth and not use it within the Kansai region if travelling close distances. I'll closer study what this ticket is all about. I'm getting my info from here:
Seishun 18 Ticket - Wikitravel