You didn't mention if you've used any wild or maricultured live rock. If not I'd read Aquabiomics article and order some or check the LFS for some. There are very complex microbial processes going on in reef systems. Only a few percent can be cultured and stuck in a bottle. The best and only sources are from nature. Here's an excelllent article on establisihing a healthy microbiome:
Studying the effects of live rock in a newly established aquarium shows that high-quality live rock promotes the rapid establishment of an effective biological filter and a microbial community similar to those found in mature reef tanks.
www.reef2reef.com
Here's some links by scientists studying reef ecosystems you might find informative:
"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title, both deal with the conflicting roles of the different types of DOC in reef ecosystems. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems
Changing Seas - Mysterious Microbes
Nitrogen cycling in hte coral holobiont
BActeria and Sponges
Maintenance of Coral Reef Health (refferences at the end)
Optical Feedback Loop in Colorful Coral Bleaching
Richard Ross What's up with phosphate"