I’m currently in Malaysian Borneo and thinking of heading out into the Indian Ocean, up to the Maldives and Sri Lankan [if I can get away with it], down to Madagascar, then down to the southern tip of Africa to round the Cape. I was thinking that it is perhaps best to sit out the SW monsoons exploring Indonesia but should I really wait until Jan for the NE monsoon?

The problem is that if you wait for the NE monsoon (December to April) in the North Indian Ocean, you risk arriving during the cyclone season (late November to end of March) in the South Indian Ocean! You should certainly not wait until January!

You may be able to leave earlier, during the SW monsoon, but you must watch the weather carefully as there is a risk of tropical storms, in the area of Sri Lanka, in October and November. September may be a safer bet, but you may have strong SW winds past Sumatra. Early in October, the SW may get lighter, so head immediately for Maldives and across the equator as soon as possible, so as to arrive in South Africa by mid-November. You would certainly have to move fast!