In addition to the documents you mentioned, you will need some form of ID. I showed my passport to the office personnel at Perkins/Toll, which they photocopied.
WARNING: After you get your CPD stamped-out at Darwin Customs you must
take this back to the Perkins/Toll office so that they know the shipping-out has been acknowledged and approved by Customs. If Perkins/Toll doesn’t see the stamped-out CPD then they will definitely refuse to ship your bike up to Dili (.. I almost came a cropper on this!)
Shipping time from Darwin ~~>to Dili takes about 36 hours. You will need to drop your bike off at the Perkins/Toll quayside depot 3-6 days prior to the shipping date.
Island hopping from Timor-Leste across the Indonesian archipelago is fairly straightforward, although it is all a bit ‘rough-and-ready’ - read this HUBB thread
for some useful information about Indo ferries, into which I have contributed a post or two. For more info click-on my signature link (below), which will take you to my blog; there's some more stuff in there about riding from Dili to Dempasar, including ferry deals.
Good luck - you'll have a blast, I'm sure.