Do you have a pic that shows where your LED's are hanging in relation to the tank? ..and also pics to show what the flow is like in there?
I continue to believe from all you have written that your alk was in the toilet for a long time. That would cover why you had issues with your chalices, and why you have so little coralline in the tank.
You are mixing corals - some of which don't mind higher nitrates (zoas, rics, many softies) with LPS and SPS type corals that won't tolerate them.
It takes a while for a tank to stabilize AND it needs to constantly remain that way with no ups & downs for it to really come into it's own. We're talking months here, not weeks.
Keep all of your parameters spot on, be patient, and good things will start to happen.