Interesting TL, i hope you dont skip too many years too fast, i dont want a good TL to die young
There are lots of issues i can see that have to be settled by 1550, and i think you have to butterfly some of your events (such as the 1565 invasion of manila), with the increased contact in that area, the europeans would probably go there sooner, and with lapu-lapu's warmongering tendency, the sulanates and rajahnate would be heavily armed ( especially for an east asian island archipelago) and would repel the europeans back.
With their tech, i can see them plausibly conquering malacca or at least turning them into a vassal (they are much closer than the european nations and have a huge tech lead now). If the 2 sultanates and the rajanate at least form a confederation or a loosely tied empire like the HRE at the very least, it would be a formidable foe and can take on the south east asian island nations.