Have you tried using the PNR on the JAL site? I'm purely speculating here, but often you have to go to the operating airline's site to get the seat. I think I've had to do that for JAL flights in the past, and haven't had an issue.

If it doesn't come up there with a booking, you may have to call AA and get the 'ghost PNR' for that flight segment. I don't remember if JAL is using a system that talks to AA with the same PNR or not. For example, I know Qantas does not and you have to get the ghost PNR from AA customer service.