So here is what I did to get out of this situation: I range the AA RTW desk and spent a moment or two convincing the agent that since I was upgrading, there would be money for AA involved and so she should consider helping me. It didn't take to long to convince her because generally they are very helpful. We went through the flights one by one to get the A class needed and at the same time, and this was the clincher for her, she put both a BA over water and an Qantas over water on AA codeshare flights (actually, the BA flight had to be on the day before as she couldn't find A on the day I was originally booked...despite EF showing A availability).

It took quite some time, but she got through it and sent it for ticketing. It came back with nothing done for some reason, so she went back to the ticketing folks again and this time it worked. All paid and now under the control of AA instead of Qantas. Yipeee.

The only problem I have now is that when I try to reserve seats, all the airlines involved (BA, AA, QF, QR) say either that the ticket is issued by another airline or that the flight is with another airline and so I have to contact them...they all say this. Anyway, will ring the AA RTW desk to see if they can help clear this up.