Not sure how you arrived at bacteria being the problem. So many good comments/questions from others regarding what might be happening.
For bacteria, I like to buy my fish food from the local sea food counter (salmon, shrimp, etc.). I mince these up and freeze. They feed the fish, but also provide a constant supply of oceanic bacteria. Sometimes I place the outer exoskeleton from shrimp and crab into a net and soak in the sump. I also dose small amounts of molasses as a carbon source. One study indicates molasses causes a population increase in a certain type of bacteria that helps break down larger waste products in tanks (fish poop). Go easy on molasses. A little goes a long way and can really crash your PO4 levels.
I also feed my system 1-2x per day of reef roids. My Goni's, SPS and LPS seem happier when I do this every day. If my PO4 gets too high from this, I dose a little molasses.
The most important factor for you corals might not be a single parameter, but stability of all parameters.
