To my knowledge, there are no boats or ferries from Peninsular Malaysia to Sarawak or vice versa, you have to fly. There are lots of vehicle ferries running to most all of the major islands within Indonesia, but I am not sure about Borneo. But certainly you will find plenty of ferries along the Timor to Sumatera route.
We looked at taking our bike on a Pelini ship from Flores to Timor and were told that if we could fit the bike through the doors (we could, but barely) and the captain allowed it, we could take the bike. Well, when they asked the captain if we could take the bike on the ship, guess what happened...yes, we could take the bike on the ship, but at a very expensive rate! It was too much for us, so we took a different route. I think he wanted over $100 to take the bike and it was about $10 or so on the ferry.
The right amount of money can open lots of doors in Indonesia though.
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