Your plan sounds amazing! I’d recommend transiting in Singapore if possible it’s a very smooth experience with a fantastic airport, while Jakarta can be a bit hectic. A 5-night liveaboard in Komodo and 7-night land-based diving in Bali is a great combo, as Komodo offers stunning marine life and Bali has diverse dive sites like the Liberty wreck and great muck diving. You could also check out other destination from this article
Indonesia Tourism Statistics 2023 - All You Need To Know For a third destination, I’d suggest either Alor or Manado. Alor is remote and pristine, with amazing reefs and macro life, while Manado (or nearby Lembeh Strait) is perfect for wall and muck diving, plus it’s easier to reach than Maumere given recent flight issues. Have a fantastic trip!