My info is from 4-5 years back, so could be outdated.
But there are probably still no ferryboats going between Malaysian peninsula and Borneo. Freighting the bike by air or by sea is probably possible, but that might cost a bit, and is usually a lot of hassle.
There should be ferries going inside Indonesia (from Java or Sulawesi), that go to their side of Borneo.
I do remember reading something about a smaller cargo boat, that someone had used to ship a bike to Borneo from West Malaysia, and thought it was relatively easy. Sorry, but I don't remember any details, and anyway it was a long time ago, things always change over there. Something like this might be the best option, if you can locate such a service from somewhere. Good luck & please update here, how you'll end up doing it!
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