I have a very good friend in Iloilo who builds boats for dive shops in Boracay.
I believe Calypso Divers bought one he built for Victory Divers.
Fisheye Divers has an 80 footer, Maruha, that was built about 3 years ago. It goes to Coron, Apo Reef. Anywhere.
He also gets boats in the 35 to 60 foot range. Any size.
As you're aware, all areas in the Philippines have their own styles. You can tell where a boat came from by the shape of the bow or stern etc.
Here's a shot of the Maruha. I was on it two years ago to Coron from Boracay. Nice boat.
If you're interested, let me know, I can get Boy's phone number to you.
You can see more of it here.
http://www.fisheye-divers.com/documents/divesafaris.html
Building your own may not be a good idea. I know an American who tried it and it was a disaster. The locals know what they're doing. Those boats are kind of works of art. Thickness of bamboo, coco lumber, where the cosco comes from....
Getting the boat from Iloilo to Luzon is only a matter of fuel.