I would disagree with the sentiment about bio-balls stated in this thread, especially in this situation. Since you're running a FOWLR setup, and not a reef, chances are the bio-balls are a benefit... especially considering that this is a pretty hefty bioload for a 55 gallon tank. I would concur with everyone about food though -- brine shrimp has next-to-no nutritional value... its somewhat like potato chips for fish. Get em some mysis, or one of the many saltwater 'formulas' and I bet you'll see improvements all around.

I also agree with justahobby -- the spots don't appear to be related to the typical color morph when leaving juvenile stage..

-Justin