Skip Pintuyan, stay on the other (east) side of Sogod Bay. If you are here in January/February it is prime whale shark season (usually), and though it's not a guarantee, you have a great chance of seeing a few. The area off Pintuyan isn't as reliable as it was just a few years ago, and if the reason to stay out there is to be closer to the whale sharks, the area is accessed by frequent in-season day trips offered by any of the bay's west side resorts. If your reason to visit Pintuyan is because it's on the way to Padre Burgos from Surigao, there is a Cokaliong ferry that will take you to Maasin from Surigao. Better yet, skip the hassle of Surigao and fly round trip Cebu to Camiguin.
As for your acr-i card: if you do get a visa extension at a local immigration office, forget about making a special trip back to pick it up. You are only staying a short time, and other than being required to pay the fees to get it, it only becomes necessary if you are renewing a previously issued 6 month visa extension. Have you considered going through the trouble of having a multiple entry visa issued in Spain, and then leaving the Philippines before your first 59 days expires for an overnight or weekend in Hong Kong? You receive another 59 day stamp on your return. There are some incredibly well priced flights out of Clark. The I card then is a non issue. You can get a 3 month multiple entry visa and the trouble might be worth it for you. If you do not want to travel to an embassy, you should be able to mail it with the proper documents, have it issued, and returned to you, and save yourself that trouble at least. You have time for that. You will almost definitely NOT get a 59 day stamp on arrival without going through the embassy process first.
As for your exit ticket from Philippines: it does not have to be within the original visa period. You just need to have one, and it can be for 3.5 months after your arrival.
Last but not least, you will be here for Chinese New Year. Make your plan well ahead and don't plan to be moving at that time if you can help it. Also be aware that Sinulog, in Cebu, is the third Sunday in January. Plan well ahead to either avoid the area entirely, or dive right in. If it's something you want to experience, it's not too early to make your arrangements.
With 3.5 months on the ground, I wouldn't be too concerned about checking most of these places off your list without moving around too much.