Couple of thoughts:
High alkalinity relative to NSW, high intensity lighting and very low nutrients has been anecdotally linked to RTN and STN. If it were my system, I would gradually bring the alkalinity, calcium and magnesium more in line with ocean values.
In my case, I accidentally bleached a superb aussie deep water acro by not paying attention and running the alkalinity into the 10 dkH range and the magnesium concentration into the 1800 range. Catching the problem and slowly ramping back down to about 7.5 dkH, Ca about 400 ppm and Mag to 1400 ppm or so seems to be helping, this colony might actually survive.
A couple of your pictures that have small patches of RTN look suspiciously like LPS coral aggression. In my case, I had a small chalice frag 3" away from another deep water acro and a orange monti digi, thinking that was plenty of separation. The corals stayed in this position for several months, and all three were growing nicely. One day I noted patches of tissue loss on the acro and the monti. That night, I examined the tank by flashlight and found that the chalice was putting out 4" long sweeper tentacles. Even though I moved the chalice immediately, the acro developed RTN and died over about a 2 day period. The monti survived and has largely healed after about a 4 week period.
Regarding feeding - a lot of us use live phytoplankton, and quite a lot of it, to feed our SPS corals. I do this nightly, at a rate of about one teaspoon of Reed Mariculture's phytofeast live per 50 gallons of water volume. It's just enough to slightly (and I do mean slightly) cloud the water. I supplement this with oyster feast about 3 times a week, at about 1/2 the dosage of the phytofeast. I also turn my skimmer off for one hour after dosing the phyto/oyster feast. Once the skimmer is back on, any remaining cloudiness clears in about 30 minutes. Note that I do this after lights out - it made more sense to me to feed the corals at night when polyps are more fully extended.
A note about dinos/cyano. I've personally found nearly immediate success in battling these pests by altering the spectrum of the light over the tank to remove red components. This is quite easy with my system that has LEDs, I just turn down the red emitters. With my fluorescently-lit reef, I changed one of two combo cool white/460nm PC bulb to a dual 460s. This system had both cyano and GHA. Both vanished within a week of changing out the lighting. You might be able to experiment with your system by putting a piece of translucent blue acrylic between your MH bulb and the reef, which will filter out the red spectrum from the bulb.