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 against
wind 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.