This one may be out of reach. It looks like SAN-NRT is only available as a married segment paired with NRT-MNL, but AA has a problem booking it. If you've already called a couple of times without success, in this situation I would move on and try something else. I think your only chance on this one is to book on another day that is available and then see if a flight change will allow you to change the date. Ideally find a date with the exact same flight numbers that is bookable, book it, then call in and ask to change only the dates of the flights. If you are lucky, the flight change booking engine may not be as buggy and it might work to change with a change search, but I would probably try to push for them not to do a full flight search for Sept 25, but just to change the dates on the flights and send a request to JAL for confirmation, basically a long sell, but made easy by the fact that you alread have all the flights in a booking and the agent only needs to change the dates and request confirmation.

I found July 6th has those exact flights (JL65 07/06, JL745 07/07) that go past the error page you hit. I would book those, and after it tickets (and this could be a problem since AA doesn't always ticket in a timely fashion), call, tell them you want to change only the dates on the flights, keeping everything else the same, so change the dates to JL65 09/25, JL745 09/26 and see if it will confirm. It may or may not, but that's about the only way I can see possible to attempt a booking on that date since you've already had multiple failures online and calling to book directly.