Two parts of the cycle are still to finish it seems. Diatoms and algae.
What he said.diatoms and algae are not definitive signs of the initial cycle being incomplete.
With the addition of your new livestock, your tank is experiencing a mini cycle until your tanks filtration restores a balance in the nitrogen cycle (ie the bacteria has caught up with the new bio load). Just monitor NH3 and NO2, run you skimmer and perform your water changes (if you are doing them.)
If you switch your lights off for 2 to 3 days your diatoms should clear up. your zoas should not be affected.
What I don't understand is that the rock was like this before I left for a two week holiday(week 6 of cycling). I left the lights off during this time and the algae was still present when I got back. The algae is just darker now that I have the lights on. The algae on the rock has been present from about week 4 of cycling. I have been running my skimmer from the beginning and have to empty it about every 5days.