I know this is a few months old post but just to share my experience with JAL website (sorry, but it was awfully difficult to navigate to put it mildly). Booked my flight using CapOne travel portal for BKK - HND - DFW - MCO trip. I was able to select the seats for DFW-MCO on my AA account. I was also able to select seats for the HND-DFW leg by not logging into my JAL account and did it as guest user. However, while I can select seats for BKK-HND, the system errored out. My next approach was just to call the AA PP phone number and requested the seats. The rep put me on hold for a few minutes and came back saying she requested the seats for me. I checked my booking once again and I could see the seats assigned. So I guess the bottom line is that, stop wasting your time trying to decipher JAL's website and increase your stress level in the process. Call and have peace of mind. Disclaimer: this may not work for everybody but it's always YMMV.