1. Book directly with JL. In my experience, AA has a very hard time dealing with any issues that arise with tickets they issue for JL flights.

2. You may be able to bid in advance for an upgrade.

https://www.jal.co.jp/jp/en/inter/se...al/bidupgrade/

3. You may be able to purchase an upgrade at the airport, but only to PE (vs bidding which allows you to go for J).

https://www.jal.co.jp/en/info/inter/apopyug.html

On such a long flight, especially with JL, I would be doing whatever I could to upgrade, it'll be well worth it.