Sorry to hear you have a pest problem. I had a similar thing a couple weeks back, where I noticed my red montipora STN'ing and didn't know what it was. After testing everything and having all the parameters look good, I wasn't sure what to do. I decided to dip the coral in Bayer and break off a few frags. Some of the frags died and some didn't, but the largest piece lived.
Fast forward to yesterday, I found a nudibranch on another montipora. Alive! So, I dipped it and all the surrounding pieces, scraped off the eggs and am hoping for the best. I think routine dipping is about the best thing you can do. Especially, if they are throughout the tank.