OK, this is not first hand experience, but if it helps.
Following a comment in Lonely Planet I found this link, I have quoted that Lonely Planet link as well because it has someone who has personally vouched for this and even provided an email offering help for travellers. The next page also contains an update about a year ago, but you may not need it if you choose to use the company link.
This does contain a ferry that is operating on 05th December 2014 (and 9th and 12th – I guess its Tuesdays and Fridays only) from Sandakan, Malaysia to some destinations including Iloilo in the Philippines.
I don’t have a complete answer, but I think you can actually get pretty far by ferry alone.
There’s a ferry between Puerto Princesa and Iloilo City.
You can get there by taking the ferry from Balabac to Bataraza and driving the rest (although there should also be a ferry between Bataraza and Puerto Princesa).
Although I don’t know any ferries to Balabac, the locals there are famous for trading with Sabah (northern Malaysia). There’s about 50km of water between Balabac and Sabah.
An alternative route would be over Zamboanga, but getting there would probably be even more difficult.
Most (not all) ferries in the Philippines are handled by 2Go Travel.
Credit:stackoverflow.com‘