This is a really good post - thank you. I've done something similar (re: exploring Japan), but on Avios fares, and explored most of the south, as well as the Sea of Japan side - ended up driving most of the Tohoku area, but I didn't know about the taxi service at Akita - that's one I haven't been to yet, so I will have to give it a try!
I echo your "upgrade to class J" comment. The less popular routes are pretty easy to upgrade on, the others less so - ITM, CTS, OKA and FUK are almost impossible.
You can do checkins at the JGC/First Class counters, btw. I've done multiple flights on the same day and nobody's ever batted an eyelid. Nice bonus is that unlike in the US, the agents can not only check you into the remote airports (so if you're doing a back-to-back HND-OKA-HND, for example, you could avoid getting out of security if it's truly a pure mileage run), but also put you on the upgrade list for class J, which means you'd be on it a little bit earlier than the rest (though status will trump you anyway).