My experience was that 99% of the time we weren't close enough to land to get mossies. The rest of the time, I didn't see any mossies so I would say the risk on board is negligible. I did get bitten twice on the single night hotel stay in Sorong on the way in. No malaria as of now. (knock on formica). Realize we are talking about malaria so my opinion is it's worth a few bad dreams (my only side effect) to avoid. I stayed in the airport transit hotel in Jakarta so no problem there.
The carry on weight thing is a moving target. The short answer is they do care and they do charge for overweight in checked baggage though really very little for the convienence. I used a camera backpack and wore it the entire time to appear "light" and just a backpack, even though it was about 19 lbs. They never checked it. If you walk up loaded with stuff, I think they (international and domestic) will want to weigh it.
Only extra tips I can suggest is bring "ear drying" stuff. I started to get an ear infection during the trip, never noted one on past trips, which started to hinder equalization. Luckily they have medicine for that on board but it would be better to prevent it. Make sure your travel gets you there a day before and there can be travel delays on the way out. Marvel at the inefficiency of the airport which has 30 (no lie) baggage porters but only one guy from the airline to pass the entire luggage of a 737 through a door in the airport to the waiting porters. Be prepared for serious heat in the airport on the way out as it can be a long process.
I'm writing my trip report and you should see it before your trip.