JAL's IT system is horrendously bad/difficult to use IME. At least using their website, I have to put in my full name, flight dates & number, and confirmation code. It also doesn't help that they have 3 different systems to look up confirmation codes (as wholly domestic itineraries use one of two different systems).
If you're booked on JAL via an AA codeshare, as far as I know there is no way to select your seats in advance.
Also, note that when looking up your itinerary on JAL, they will drop your middle name (if any), even if it's on your AA ticket.
Edit: As for
It was escalated to a supervisor at my request and he was not one of your usual friendly agents, but I explained the situation. He told me that I have a contract that states I cannot get a seat assignment until I get to the airport, nor can I get confirmation until then. That was not the original agreement I reserved. I was able to have seat assignment and able to upgrade.
sounds like a HUCA situation.