I'm hanging around in Sumatra at the moment and have been thinking the same thing. I've been asking around about ferries and that but solid information is pretty hard to come by. The best thing is to just turn up at the port at ask what boats go where. But going to Sulawesi/Borneo I think is best from Jakarta or Surabaya.
I'll try and make a move up there in May or June so I'll post back again when I've found out something, or give us a shout when you're in the area and we can have a go together.
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