I can offer some insight as I just came back from Japan and spent a chunk of that time doing mile runs. I grabber over 32K fops over the two weeks I was there.
- You're going to need the trips back and forth between US/Japan to give you a good head start. It 14,246 FOP if you get 100% miles from JFK<->NRT (Which according to the factory tour is their longest and toughest flight)
- I found when booking Global explorer fares on the JAL Site, JAL will not let you book more than 2 legs on the same day, even if you try to break it into 2 different trips. I was going to originally do HND->FUK->SAP->FUK-HND in one day, but JAL said no to that.
- As someone pointed out, Tokyo<->Naha is the most miles you can ding in a domestic flight there, but be advises that not all flights have 1st Class.
- Always grab for J upgrade if you can't get F. The 10% bonuses add up.
- Also, make sure your time there doesn't overlap over any major holidays :P. While I was in Japan over 2 weeks, I only had 5 days I could actually book flights on as every other day fell during Golden Week and good f'ing luck booking then (Before anyone asks, yes I was aware of it and had wanted to sync up with Golden Week to match my friends in Japan who were of those 10 days.)
Good luck, I've been JGC over 10 years, would not trade it for the world and especially not for an AA Elite status.