Indonesia
 

For anyone that has ridden all or most of Indonesia, could you tell me if there are ferry crossings between all the islands? For me and my bike? If so, in which towns are the located?
If not ferries, will I have to freight the bike and fly or passenger ferry myself separately? Obviously a ferry with me and my bike is ideal.
How far East should I go until I ship to Australia? Then do I go to Darwin, or elsewhere in Oz?

We've done Darwin to Malaysia via most of Indonesia and Borneo. Here's the ferries we took in Indonesia:

Kupang (West Timor) - Larantuka (Flores) weekly.
Labuanbajo (Flores) - Bira (Sulawesi) weekly.
Pare Pare (Sulawesi) - Nunukan (Kalimantan) weekly.
Pontianak (Kalimantan) - Semarang (Java) weekly.
The Pontianak - Surabaya ferry no longer runs.
The Java - Sumatra ferry runs hourly.

This was done between March 2009 and October 2009.

The best thing is to carry on heading East until Dili then ship the bike to Darwin however you will have to fly.

Ann

Plenty of ferries in Indo
 

We have two good friends that did all the bigger Indoneisan Islands in the opposite direction. They confirm the above that there are ferries to and from all islands and they used Perkins shipping from Darwin to Dilli.

Good luck with the traffic I hear it's a nightmare.