Indonesia seemed like a country, where at least your vehicle´s point of entry really needs to be chosen carefully, or you might run into a lot of trouble, or at least delay. Penang <-> Belawan, and further east, the land border between East Timor and (Indonesian) West Timor - these two routes seem to be the ones, that most travellers use. May be that is also the reason, why few have had significant trouble with the customs at those crossing points. For us it took some 10 minutes to clear the bike in Belawan - after all the horror stories I´d heard, I was expecting it to be a lot worse!
I don´t know, how it´ll work out, if you use Belawan as an exit point.. but I did meet people, who had come that way, and thought it was ok, except maybe for some scammers at the port.
One thing to find out before you set off is, will a carnet be required, if it is(?) an Indo-regoed vehicle, that you´re taking to Malaysia. May be you won´t need it if coming from another ASEAN country, but I really don´t know. Malaysia is relaxed about the carnet on land borders, but shipping in could be different.