I had a fellow english couple stop with me for a few days in Jogjakarta (central java, Indonesia).
They had shipped there bike from Darwin to East Timor and then gone through to Timor Leste over the land border.
From what I remember its was a realatively straight forward and easy process.
You now get a 30 day visa on arrival in Indo which you can extend at any imigration office for another 30 days. When your time is up on the visa get a cheap trip in and out of the country to re-new.
You could also get a 60 day social visa (which can be extended 4 times, a month each time, so 6 months total) easily through an agent in singapore but that requires a sponsor so is a little complicated.
Here is the link to Keith and Ellen's blog page covering the border crossing into Indo...
If you do come through theres a room and a beer at my place