Yeah, one nanban trade port is going to cancel out the effect of several monks, never mind just the one low level one, so trash it asap.

In addition to the nanban trade ports, I dont think religious buildings get autodestructed when you conquer a province like they did in, say M2TW. So check for those and destroy them pronto. Replace any christian buildings with temples (at least second level if possible). Then spam with multiple high level monks.

Well worth softening up christian provinces with monks *before* you invade. This gives you a chance to boost your monks levels (via incite uprising/demoralise missions) which makes a massive difference to conversion rates.