You're in for a process that will likely still end with a lot of casualties... Pull everything from the main tank. Remove all areas where there is no tissue. Run a thick bead of glue around the spots you cut away. Dip everything. I use TMPCC (and swish swish swish). I tried Levamisole a few years back and it was pretty tragic. They were gone, though. Keep the acros in a QT with weekly dips and inspections. Remove all tissue left in the tank from encrustation on the rocks, too, as that will extend the 'out of tank' time (continued food source). No guarantees, but it'll make you love the idea of QT...
Going forward, always QT. I have several systems that are somewhat dedicated (no SPS in a few, no LPS in a few, no zoas in a few, etc.). If I don't set up a dedicated system for QT when I know I have some corals coming, I might put Acros in a system with no acros, etc. I usually set up a separate tank, unless I unexpectedly buy or only get a few frags. If going into an established system (devoid of like genus, etc.), they get a dip and inspection for a few weeks before going to the display. If they are going into a dedicated QT, I may skip the dip to reduce stress. I have a hard time with dedicated QT's holding parameters over time, so I sometimes just inspect for a longer period of time to reduce stress (no dips unless I see something). Removal of bases and dead skeleton before putting them into a display doesn't hurt. That takes away more potential egg areas. In addition to TMPCC dips for AEFW's, an Interceptor dip is a good idea, too. Red bugs aren't really that big a deal, but they can do some damage. If you can knock them out on the front end, much less to worry about. It's a lot of work, but when you lose some of your prize pieces to nudis or flat worms, the constant pain of QT'ing starts to outweight the short term ease of just dropping in the tank.