Thanks for the responses. That was what I was looking for.
I plan to talk more about my itinerary in a separate post, once I fill in some of the gaps a bit more. (having these questions answered certainly helped with some of those gaps)
But, since it was asked, this is our first trip to Japan, so simple stupid is good this time around. We'll be there a week, which is why we're thinking of a JR Pass. Since we'll have spent the two weeks prior on a family trip with my fiancé's parents, brother, brother's fiancée and her son, the Japan trip is intended to be a nice chance for the two of us to explore and rejuvenate together before heading home and back to our busy lives.
Once again, thanks a bunch for the info!