You'll likely need to beef up your clean up crew, because now that you have light and nutrients available, other simple organisms present will exploit them too. It's ok, you just need to work your way through them and you will end up with a clean tank that's well balanced and everything is growing.
Your current clean up crew is probably greatly outmatched since they were in a very low nutrient system where there wasn't much available to support much microflora.

Basically what we have done is introduced all the neccisarry ingredients for life to flourish and it is! You're corals will follow suit. You just have to get through the uglies first.
One of the best things against the brown crud in my opinion are the dwarf cerith snails. (Diversity in a CUC is one of the most overlooked things in our hobby, I feel).
You're getting there and making progress!