I'm also interested in the Indonesian weather
as we should be heading that way next year.
What you're planning clearly falls into the monsoon season. Lonely Planet has a webpage
that gives an overall coverage.
It does look like it could have a fair bit of rain at that time of year.
I have no knowledge of sea and wind
conditions in Indonesia
. I dimly recall
a report of a cruising yacht foundering a few years ago, possibly due to seas such as you've been warned about.
My own, non Indonesian, experience suggests that if you have current
this would give a short, choppy, or messy sea. With many islands it is very probable the a wind against current
situation could occur. It may be possible to work this out from the pilot charts
or local knowledge could be gold.
From the perspective of an intending cruiser the biggest problems that I would anticipate would be that the weather
could be very, very wet, and that a cyclone could develop with little or no warning being received.
There is the Badan Meteorologi, Klimatologi, dan Geofisika (disingkat BMKG)
that should give warnings. Unfortunately it is in Bahasa Indonesia
, a language in which I am far from proficient. An English
version is under construction.