The only miles that you can use for upgrades on JAL are JMB miles. There is an option to do a cash upgrade to PY day of departure if there are seats open when you check in. I find it rather on the expensive side, on the US routes US departure is 350 USD per person and Japan departure is 40,000 JPY per person.
JAL Y is most likely the best Y product out there, pitch is 34" 787s are still 8 seats per row, 777s are still 9 seats per row, and no plans to change that. I would suggest that you save the upgrade costs and get a good dinner (or several) in Japan for that money instead.