I have now used the 16 segments :
CGK-HKG-KIX-HKGx-LHR-MCT-LHR-IST-LHR-YVR-JFK-SJO-DFW-MIA-JFK-HKGx-CGK
So do I now ring the AA RTW desk, pay for the ticket with my Australian amex and they issue an E ticket?

No. Ring the RTW desk and have them set up the itinerary and assign it a PNR. They will need to send it off to their rates/tariff department (Dublin) where the wizards will compute taxes and fuel fines, etc. The RTW desk should have the final number in ~24 hours but it can vary.

Once you have the price and the PNR you will need to contact an AA office in Indonesia (or a travel agent) in order to arrange for payment using your credit card. They may want a fax of the credit card front/back, or they may want a wire transfer, depending on local policy. The ticket has to be issued in Indonesia.

As a "control" or for comparison purposes, meanwhile you could put your itinerary into the Oneworld Explorer booking tool and see what the final number is. I think everyone who frequents this board would like to know the variance between the robotic fare and the AA fare.

Well, maybe - have we had a definitive answer on the "Issue in Aus at ex-Indonesia price because there is no ex-Aus AONE3 price" question? Must be worth a call to AA Australia to see if they'd do it.

I am now totally at the end of my tether!!!
I have spoken to FIVE different agents at the RTW desk in Dallas and they are refusing to book the itinerary
CGK-HKG-KIX-HKGx-LHR-MCT-LHR-IST-LHR-YVR-JFK-MIA-SJO-DFW-JFK-HKGx-CGK
They are all saying I can only have 1 stopover in the continent of origin , despite my stating the rules

"You are allowed to take two stopovers in total within your continent of origin in order to get to or from a gateway to begin or return from your international travel of which a maximum of 1 stopover is permitted in each direction in the country of origin."

They seem to be confusing country with continent. I asked one agent to speak to a supervisor and the supervisor confirmed what the agent said. !!!!
(despite it being fully validated on the oneworld site)

So, giving up I decided to book online and pay the extra fuel taxes and got to the point of payment and couldn't pay for the ticket with AMEX, they only take Visa, Mastercard or Diners. My Visa limit is not high enough to pay for 2 AONE tickets.

I'm ready to throw the whole thing out the window. Any suggestions ?

Prepay your Visa card would be the obvious one - you can take your Visa card into positive balance without a problem.

Although I am really quite surprised about the AA desk - I have never had a problem with them. The rule is absolutely clear so I can't see how they can refuse. I wonder if the reall problem is no over-water AA flights in there?

Christep, you are brilliant! Loaded up my Visa card and it is booked.
With regard to the RTW desk, I didn't get past the Asia sectors before they rejected it. I was told that after CGK-HKG I had to go straight to LHR.

Thanks for all the advice everyone.