We spent about 5 months riding the length of Indo. No trouble anywhere. Lots of friendly people. The only exception was when we stored our bikes in Kupang with a family, somebody stole some stuff out of a pannier.
Yes, Flores is slow going, but so are Sumatra and Java, unless you want to do battle on the main roads. Plan to fly out and get new 2-month visas once or twice.
Biggest danger, as usual, is the traffic. Like in India, it is expected and necessary to use the horn a lot, as people never look back.
A friend who lived in Philippines and Indonesia advised me to avoid the area around Danau Poso on central Sulawesi, due to ethnic strife.
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