Your routing looks valid to me as well.
AMS-HKG-KUL-SYD should be better than AMS-LHR-KUL-SYD if you want to avoid MH.
however I keep getting push back on the number of transits I have, and they keep trying to push out the dates of my flights back to Syd so that there are more stop overs and less transits
Not every agent knows/agrees that stopover can be used as transit - ask them to hold the itinerary (and the seats) and call again
Insist them send the itinerary to ticketing to assess the validity
Also I got a quote on my taxes from her... $7565HKD! What changes can I make to my itinerary to bring this down a little, it seems extraordinarily high!
Their CS can never get the tax right - the actual amount of tax can be quite different from what was quoted. In your case, it is quite likely that the agent has included the UK APD.