Just got back from my second trip to Japan in six months, I was there for three weeks and probably used about $30,000 worth of trips with my JR pass! I've always managed to satisfy my rail interest by going to a large city about 1000km away (Sydney, my city has no passenger rail ) and I've been able to ride their network of intercity trains (4x 150km lines, 3hr travel time) for only $2.50 a day as they have a special ticket for people on welfare. I got kind of bored with the system because it's pretty simplistic (but very scenic) and set my eyes on Japan. I delayed it by several years because 1) I never thought I could afford it, 2) I have a police record for "borrowing" council/county boundary signs when I was 17 and 3) I've been on heavy-duty sleeping medication until recently, so much so that a doctor would never prescribe enough to take anywhere for weeks at a time. Even now I had to apply for a narcotics certificate.
My first trip was October last year, with the whole police record thing I was shaking that much at immigration that it took four tries to read my fingerprints, once I was through with that I had customs very interested in me ticking yes for the drugs question. When I gave them the narcotics certificate everything was fine. Just like my first trip to sydney, I never ventured more than about 2 or 3 hours out of Tokyo. I was only going to stay five days but the heat caused some sort of rash that made it painful to sit down, so I stayed a few more days as I simply wouldn't have been able to sit on a flight for 10 hours.
My second trip started at the end of April, I stayed at a guesthouse about 20 minutes west of Ikebukuro for only $U.S100 a week! I wasn't afraid to miss the last train home this time, so I took advantage of capsule hotels, and went to Sapporo, Osaka, Kagoshima, Tottori (my favourite small city) and several other places not on the Shinkansen network. I was going to travel on all shinkansen lines just to say I'd done it but by that time I was pretty sick of "Ladies and gentlemen, we will soon be making a brief stop in..." - btw the English announcer for the shinkansen is Australian.
The trip was a blast apart from not being able to get a window seat sometimes during golden week (I'd just sneak into the green car a couple of times). I've always had rail questions about Japan but got kicked off of reddit for asking too many of them! They have a Japanese rail sub but it only gets checked a couple of times a month. I'm betting that you guys will be a lot more friendlier!