Can you tell me about your lights?
I'm not 100% sure but have a paly frag doing the same under too much light.I moved mine lower to see if they will do better.
Budget wise,I would go with a RKL for 125 bucks.Control your lights,temperature,powerheads and many more options.
http://premiumaquatics.com/aquatic-supplies/RK-30-0012-001.html
They are going to re-design the skimmer to fit the Nuvo 16 and 24 because those tanks have become so popular.I haven't checked back in awhile but it could be available already.
Typically,most people use 4 modules on 6ft. tanks.I'm not familiar with that fixture.Actually,that's the first time I've heard of an LED fixture that spans the whole length of the tank.
If you go with that fixture you could always go with lower light corals on the very end of each side..
Are you talking about those dark spots on the sand?
I haven't a clue on what type of algae that is.I wouldn't worry about it during the cycling period.
They are too sensitive so I removed mine completely.The spewing of microbubbles or overflowing from just the smallest amount of food or epoxy drove me nuts.Water changes will have to do until Cadlight makes their nano-skimmer work on the nuvos.They are suppose to be working on it.
Never tried there reactors.I swear John's skimmers are too awesome for words.Simple design with a self cleaning venturi.I ran one for 5 years never having the venturi hiccup or clog.