A different question is: how early does one need to get to the airport in order to transfer and get checked in for an international flight?
I would leave at least 3 hours for your connection time, longer if possible. Indonesian domestic flights are often delayed/cancelled due to weather, equipment issues etc. If you miss your connection to your international carrier, you will be left scrambling as they take no responsibility for missed connections that are not on the same ticket. Our strategy for Indonesia has always been to plan an overnight stay near the airport when connecting to our international flights home, to leave a buffer for Indonesian airline fubars. The airport hotel (in the terminal) at Jakarta Airport is clean, quite nice and budget-minded for a quick overnight. For a longer stay, you might prefer the Sheraton Bandara - they run a free shuttle - the hotel is about 10 minutes from the international terminal, and has a very nice pool area, restaurants and spa.
Also, we recently flew Express Air from Sorong to Jakarta via Makassar. These were the worst flights we have ever been on - the 737 appeared to be significantly overweighted departing Sorong (plus it was very hot and humid), and there was a moment that we really thought they would not get the thing off the ground before hitting the end of the runway (after which there is water). Once upon a time I was a flight attendant, and I do not recall ever taking that long to get the nose up on a 737. Make sure your seats are not in the back of the bus - the stench from the toilets was unspeakable, and there are no overhead bins over the last two rows, so you will be fighting for space farther forward for your carry on stuff. As someone else mentioned the legroom is unbelievably tight. I would look into the cost to upgrade to Business Class - they do not have a separate cabin, just a row of more spacious seats, but I wonder if by the time you pay the baggage overages you might have been better to book Business where you get a larger allowance.
The checked baggage allowance for the 737 flights on Express Air was 20kg per person - overages are very expensive - we paid $100 for our 25 kg of overweight.
Fwiw, we were told by a Canadian living for several years in Indonesia that some of the airlines (Garuda and Lion Air) will give you an extra 10 kg of allowance if you tell them that you are checking your dive gear. This worked for us Manado to Ambon via Makassar on Lion Air, where we checked in an extra bag at no charge. Ymmv.
You do know it is a long, fairly exposed ride out to Misool right? Your wife will want to make sure she takes some serious seasickness meds. The area is very, very beautiful, and the diving even more so.
I hope this helps,
Judy