I have not been to Lembeh but I have been to Dauin and it was exceptional
As an Indonesian Combo I would try and squeeze a muck diving destination with some reeefs
From a practical point of view most likely your itinerary will center around Bali as most flights leave from there or otherwise from Jakarta
Also in September or October is not really the perfect time for Raja Ampat but you could try
Bali + Komodo
Ambon + Flores
North Raja Ampat (south is windy) + Lembeh
The North Raja Ampat + Lembeh can also be done land based you don't need to be on boats all the time
As an Indonesian Combo I would try and squeeze a muck diving destination with some reeefs
From a practical point of view most likely your itinerary will center around Bali as most flights leave from there or otherwise from Jakarta
Also in September or October is not really the perfect time for Raja Ampat but you could try
Bali + Komodo
Ambon + Flores
North Raja Ampat (south is windy) + Lembeh
The North Raja Ampat + Lembeh can also be done land based you don't need to be on boats all the time