Long term solo backpacking - Java, Lombok, Flores, Timor, possibly Maluku and Papua - advice welcome

The ease or difficulty of getting visa extensions varies from office to office.
Read the visa link in my signo line for more info on visa matters.
If you have a RT ticket from home to Indonesia for a no longer than 6 months period, you could use that for all your visas and extensions.
South to North Sulawesi to North to Central Maluku to Raja Ampat is a great route, but takes time to cover.
Your budget is not rock bottom, you could spend less in most places and then able to afford a shorter period in Papua.

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