If you are using the Explorer fare on a route which costs 10,800 yen, you might also want to take a look at the Oneworld Yokoso fare
oneworld Yokoso/Visit Japan Fare - JAL
Some blackout dates and conditions like flying Oneworld to/from Japan but it's booked as flexible economy. There is a booking fee, from memory around $60 and you need to call up. Explorer fare is booked in G class which I believe doesn't earn anything. Please do let me know if I'm wrong though so I can save some $$ lol
I used this rather than the Explorer fare from HND - cough and that gets 20SC each way. There's also more availability on flight times than Explorer and flights can be changed. I was told your first flight can't be changed to a later flight but can be changed to an earlier one at the airport if there is space. Subsequent flights can be changed earlier/later. Might not be for everybody but if you are not going to use a JR pass and want some SCs, this can be an option.