I agree with Lone Ranger and Snake Boy about against buying bike in Indonesia. My opinion you should start either from Thailand or Malaysia and tour the whole peninsular (Singapore, East Malaysia, Thailand, Cambodia, Laos, Myanmar & Vietnam) on the same bike as the immigration & custom between these countries are quick and less hassle, at least on Malaysian registered bike.
Once you've completed this, sell the bike, get another in Indonesia and start touring the country, then you'll save a lot on ferries, carnet and the immigration papers.
Myanmar requires a tour, even on a Thai registered bike. The only exception to this is limited travel near the border (only applicable to Thai registrations) but this presents immigration difficulties unless the OP gets a Myanmar visa for a several day 'tour' of Tachilek, in order to avoid Mae Sai immigration refusing his exit, because they believe him to be a 'visa runner' (visa-free exit for Myanmar and then return to the Thai side without a Thai visa is not allowed at Mae Sai). Many Myanmar travel agencies can assist in arranging a tour, it's quite straightforward these days just that it costs a bit of $$
Vietnam also requires a tour and reportedly also an escort vehicle (according to a 2014 article from TTR Weekly).
Singapore is OK for Thai and Malaysian registered bikes. All others require a carnet.
Malaysia is fine for Thai and Singaporean bikes, Indonesian ones may require a carnet hence I agree with the other posters that Indonesian bikes should not be brought to Malaysia. Probably the only realistic way would be to drive across the land border in Borneo, as the only inter-island vehicular ferries likely to be available would be domestic islands. Even though the Medan to Penang journey is a lot shorter than say Java-Borneo (Kalimantan) but being international for whatever reason no vehicular ferries are available, only passenger ferries. Then from Kuching in Malaysian Borneo to the mainland put your bike on a vehicle ferry, if available; but I have no knowledge of this. To avoid this uncertainty, forget about trying to bring an Indo bike to Malaysia, even if you could find a way to bring it to the Malaysian mainland, you'd hit a roadblock heading into Thailand with the new tour requirement, not to mention Myanmar and Vietnam (and of course China if you wanted to go there).
Cambodia is good for entry at only 2 border crossings, irrespective of the registration of your bike: Hat Lek (Khlong Yai)/Koh Kong (Cham Yeam) and Chong Chom/O'Smach. Ban Pakkard/Pailin (Prom) is a maybe, but not worth trying giving the much greater certainty of the other two crossings. Re-entry into Thailand can be made at any crossing though I wouldn't bother with Ban Laem. The Laos to Cambodia crossing is hit and miss unless you're on a local Laos or Cambodia plated bike, though heading from Cambodia into Laos is much more likely to be successful than heading in the other direction where Cambodian officials are known to refuse entry point blank.
Laos is a problem at some crossings for motorcycle riders. The 3 Sayaburi borders require a tour organized by a Sayaburi based travel agency. The most recent report I read suggested that the Lao side at the Huay Kon/Nam Ngern crossing in the north of Sayaburi near Hongsa still won't allow entry to motorcycle riders even if they come on a tour. Phu Doo is OK on a tour, Ban Nakraseng (Tha Li)/Nam Heuang is the same (no independent entries or exits). The 1st Friendship Bridge - Nong Khai/Tha Na Leng (Vientiane) border allows bikes across that are 250cc and above only, although heading back to the Thai side smaller bikes are OK. I don't like the Vientiane crossing for entering Laos because it's slow, there's a lot of traffic and people and customs usually only give you 14 days for your vehicle unless you insist on 30 days and restrict you to Vientiane (unless you can read Lao you won't know that's what it says on the form). All other crossings give you 30 days and freedom to travel the whole country without asking. The 2nd and 3rd Friendship Bridges require a permit for bikes to cross to the Lao side, the 4th Friendship Bridge up in Chiang Khong/Huay Xai is fine but they will charge you 500 Baht for an escort. The most hassle free crossing for a bike is down near Pakse at Chong Mek/Vang Tao.
I agree that a Malaysian or Thai bike is best for this trip - Malaysia, Thailand, Cambodia (with conditions as noted above) and Laos (with conditions) can be entered without making any pre-arrangements.