I´ve shipped by air from Bali (to Perth). But I don´t recommend doing it, because first of all it was expensive. Or to be more specific, the critical point will probably be, can you find an aircraft, where the loading doors are big enough to load your bike/crate. We couldn´t, and so it flew Bali->Melbourne->Perth, a total flight time of around 10 hours, whereas the direct flight was only 3 hours. You can imagine, what that does to the costs!! I don´t know, if you´d be in a better position, if you wanted to fly to Darwin.
It should also be possible to get the bike on a truck to Surabaya (Java) and then by sea to Oz, but expect that to take 4-5 weeks.
The cheapest and most hassle-free option still would be to go to Dili, and use Perkins cargo ship from there, I think.
More details here (starting from about the lowest 1/3rd of the text there):
MOTO1 - Matkalla
edit. (we were originally going to Darwin, but a couple of Aussies convinced us, that weather-wise Perth was better, because the north had had a very bad rainy season... but this was back in February -08).