Theres no problem getting from Thailand to south Indonesia. You ride your bike through Thailand into Malaysia. Then you need to ship your bike over to the island of Sumatra in Indonesia. The most common way to do this for overlanders is to use Mr Lims "onion boat" from Penang to Belawan. Mr Lim has freighted hundred of bikes so you can trust him. His ships were stopped for a while by government but seems to be going as normal now. Another option is a passanger ferry from Port Klang to Dumai - I think it was. Theres a thread about thia option in the "Southern Asia" section.
Between the different islands in Indonesia there are roroferries and transport are easy. Between the last two islands (Flores and Timor) there are only 2 ferries pr week so you need to adjust to that and the standard are not exactly european but its all a part of the adventure. Most overlanders ride to Dili in East Timor and ship their bikes to Darwin in Australia from there. There are heaps of threads about this in either South Asia or Australia/New Zealand sections on this forum.
Indonesia is time consuming but a fantastic country. Probably the highlight of my trip from Norway to Australia - so dont miss it!