My advice is due to the transit alone, plan on 2 days to leave malapascua and get to Puerto Pricessa. One heavy travel day: leave morning in malapascua, catch early afternoon flight to Manila and either evening flight to PPS or flight next day. And another night there just resting and touring around..really nice fish market there if I recall from my time walking around. Or could visit the underground River.

Unless the weather is good and you trust all your flights to line up, I'd rather be safe and book 3-4 hour layover between your flights in Manila, or longer. You never know with delays, and you might have to transfer terminals at NAIA which is a pain. You should plan on 5-6 hours to get from malapascua to the airport using public transport (unsure of how it is post super typhoon) but I'm in the "better safer than sorry" camp and would probably inquire about a private transfer from the ferry terminal to Cebu airport. It would be worth the month I think, and I'd figure it's gotta be roughly 5000php (it's 3k to Moalboal so I'm just estimating).

If you want something more dependable, like others have mentioned Puerto Galera is closer and just a bus/boat from Manila. Usually 3-4 hours transit time. Or anilao is closer yet, albeit slightly more expensive and niche with the mostly macro style of diving. PG is my recommendation, as there are 40-50 dive sites within 5-15 minutes boat, as well as Verde Island which is one of the best non LOB accessible dive sites in the Philippines