My bike in front of Mt Bromo, the famous Volcano on Java island.
I crossed over Indonesia and did quite a bit of touring there, approx 13 000 kms in 2015. I shipped my bike over from Penang to Belawan, near Medan and rode on Sumatra, Java, Sulawesi, Bali, Lombok, Sumbawa, Flores and West-Timor and into East Timor and then shipped my bike over to Australia.
It was a fantastic adventure and a really really great experience.
All I can say is have a lot of time to spare. This country is huge and roads are not so good and narrow and traffic are at times insanely tight and chaotic. Average speed is at best 40-50 km/h - sometimes less. Dont count on doing much more than 300 kms a day most places.
Ferries - ha-ha I can write novels about ferries in Indonesia, the time a huge rat stole my food in my cabin on the Makassar-Surabaya crossing or when I had to sit 18 hours on a mooring bollard because there wasnt any other place to sit on the Larantuka-Kupang crossing and had to climb over a huge pig in a temporary cage just to go to the loo.
Just ask specificly what you want to know and I will try to answer.
Theres also much knowledge on the Horizons unlimited forum/HUBB site, south-asian section.