Hi Bob:
Interesting idea.
Couple of wrinkles, but money and time can overcome:
1) I believe entering Indonesia would require a Carnet.
2) Thailand transit on foreign registered motorbikes (except Malaysia and Thailand) would require the approved gov't permit with approved route, timing and guide(s). See earlier post re: Dr.'s examination and Driving Permit for residents of some countries not signed on to IDP.
3) If renting a motorbike in Thailand to take out of country the options on places where rentals could be obtained is small. I've done it, but some hoops had to be jumped through. For instance, many rental companies require you leave your passport as security for the motorbike.
An option: Rent a motorbike (it likely will be small, under 250cc) on Bali. Many will say it can not be done (renting and taking off the island) but I've done it, and kept my passport with me, not leaving it with the rental agency as security. Time changes rules and regulations, but the rental agency I used on Bali prepared the paperwork to leave Bali that was needed to board the ferry, and offered to do it again. I went to Java, and back.
Just some random thoughts. Lotta hoops to jump through, but doable.
Dr. Gregory Frazier
Chief, of the World Adventure Affairs Desk, CITY BIKE magazine
Entrant #9 and Successful Finisher:
The World Motorcycle Adventure Tour and Travel Rally