With a POD after 1549 (the arrival of the Jesuits), the challenge isto have at least 10% of the Japanese population at least self-identifying as Catholic in 2000. Bonus points if it is 15% or higher.
Have Spain or Portugal conquer and hold on to Japan for over 100 years, that might do it.
Have you been playing too much CK2 or possibly Kessen 3?
Anyways have them conquer the island (or much of it anyway) and not act like assholes to the Japanese, that'll help substantially
Japan did not go down to European colonialism ITTL, which is essentially a giant Euro-wank. What would make European colonialism in Japan possible ITTL?
This would probably need a POD where Spanish invasion of Portugal does not to occur and the are Dutch preoccupied with the Spanish or English.
Spain was on good terms with Japan long after the Iberian Union. It was Japan who chose to isolate itself, not a lack of interest from the Iberians or the Dutch driving them out of the region.
Having it stay disunited seems like it would be a good start to me.
Even then. The 100 or so Iberians would need some serious ASBs help to take over a disunited Japan. Unless things during the sengoku are so awful that foreign or foreign influenced rule seems OK. Which is ASB for japan