If the spots aren't raised then it could just be stress spots, if they are raised however that could be Ich. I read an article that they would tend to blotch or spot up if stressed. As far as bringing down it's stress level maybe turn off the lights for a while so he can adjust to the new enviroment. I'm assuming you have plenty of live rock for it to hide in? They do take time to adjust so be patient. If it is ich you can raise temp a couple degrees in tank and soak food in garlic, metronzola, and focus, or move to a QT.
Hope this helps
Nate