We went Bali->Perth at the beginning of March ´08. We were originally planning to island-hop further east all the way to East Timor, but...
- they tried to kill the president & prime minister at exactly that time, resulting in fighting in and around Dili;
- it was the rainy season, and boat timetables etc., were anyones guess (the Pelni ships really were a joke!) and you also needed to keep in mind, that even the worst rust-buckets will sail in any weather, so I got a bit uneasy about the thought;
- we were running out of our 30-day visa-on-arrivals. Wouldve got 60 days from Malaysia, but we were too stupid to understand, how slow travelling is in Indonesia!.... I actually heard visas could have been extended ´unofficially´, by paying some considerable amount of money, but never tried this myself.
There were supposed to be some small cargo boats maybe going to Darwin from Kupang, maybe some time, and who knows if the skipper´s a nice guy, then maybe you´d be able to agree on a price to transport you bike. But no-one seemed to have anything solid on those in Bali, so once again would´ve needed to get to Kupang first to find out.
The solution: Quantas, hugely expensive airfreight (nearly 2000 US, because only possible via Melbourne!!) from Bali to Perth. Really needed a few days to swallow that, but as I said, at that time all other options became just too uncertain, and possibly dangerous (East Timor may now be ok, but I have no info about that).
The cargo companies in Bali said it would´ve also been possible to freight the bike by ship from Surabaya or Jakarta, to at least Sydney, but even that would have taken an estimated one month, nevermind if we would´ve wanted to get it from there to Darwin or Perth. This would´ve been about 1/4th of the air price.
If East Timor is do-able, then probably the Perkins line from Singapore to Darwin would be a good choice, at least I´ve heard many people have used it. Indonesia is a wonderful country, not to be missed, if you´re in the area.