So a have a somewhat update again.
After trying one more time this morning
i asked if they could just refund my AA flight - Which she said she will, took credit card details to do the cash side, and said i would be refunded 101600 pts for that flight.
(for reference whilst i initially did have a Classic rewards one world flight, it didnt hit the miles to be a full 318,000 pts).
So the JAL Flight that i cannot get an agent to book for me, if i book seperately is only 90,000 pts. And everything i read states it doesnt matter they are on seperate bookings, baggage still gets checked through, and can get the Qantas Desk to print both boarding passes at check in at first flight (BNE).
So am i missing something here, or do i just make it seperate online bookings.