Ring AA and get the Amadeus PNR for the QF, QR sectors and there should also be a 6 digit number for JL that you should be able get from them to use on their website to retrieve the booking.

The QF website will often allow you to select seats on the other carriers, ditto QR.

The only time I have had issues getting seats online is when the flights are codeshares. In that case I needed to call the AA and get them to assign seats.