Biggest problem will getting into/from New Guinea from Indonesia and then travelling there by road/track. Most freight goes into Papua New Guinea via Australia, the West Papua region of New Guinea is part of a cessionist struggle with Indonesia at present so foreigners may not be allowed or welcome if the East Timor experience is anything to go by. Smaller boats do the coastal runs - but who or where is anyone's guess.
You are probably better off going without a bike and just getting boats and buses/hitch hike.
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