Wowowow... that's a long trip that combines many flights and different season patterns.
First off you didin't mention at what period you'd like to do this trip. Maluku (Ambon/Kei) seasons and Komodo or North Sulawesi won't match on the same months unless you go in a specific time frame in October/November.
Let's check out your itinerary :
- Bali 6 days is easy to do but with a non diver you could even spend more time.
- Komodo needs a flight from Bali but 3 days leaves you only one day diving which is much too short, Komodo is the best dive/snorkel place of your whole trip, it deserves a few days more IMO.
- Then Back to Bali and Makasar you've lost one day flying. Tana Toraja on 4 days is fine for trekking, cultural tours, I did this already, the rice fields and how you're welcomed in the villages makes it a fantastic trip, you don't need to participate to funerals and kerbau slaughter . Better take a private car, lots of local agencies propose 4-5 days private tours.
- Togean will need aditional transport/flying ferry not sure about the effort.
- Bunaken is not a beachy place, I don't take the diving up to Komodo (not even Bali if you ask me). Bangka would be much worthwhile (Murex or BlueBay have really nice beaches! Or even Coral Eye for a more intimate atmosphere.) The snorkeling and the diving are great there. Needs 5 days to get to and enjoy the diving. My advise : skip Togeans and do Bangka directly flying from Makasar to Manado.
- Now Maluku is another kind of animal. Very worthwhile but hard to travel because you change the airline hub, so you need to get to Ambon to fly around Maluku (hence fly from Manado to Makasar then Ambon if there is tsill some flight connexion). Skip the stay in Ambon, your wife will hate it UNLESS you find a way to stay on molana island, perfect dream island (but NO diving, only snorkeling).
Kei Kecil (Tual airport) has only beaches.... but what beaches!!! Pasir panjang is spectacular, probably the most beautiful in the world!!! No diving or difficult to find though, I don't know whether the operations have resumed, very little snorkeling, it's all sandy.
You forgot (or skipped) the most interesting islands in the whole country : Banda islands, it's a short flight hop or a longer fast ferry ride from Ambon, much much history, very nice walks, snorkeling and diving, best food in the whole archipelago.
I can go on and on, but you need to inform about the season you will go to check whether it's feasible.
Edit : I have read your title, you are looking for June/July hence forget Maluku, it will be raining bucketloads , high waves in Banda islands.
That will be good for Bali, Komodo and Sulawesi