I would look for rust on anything....power heades, pumps, scrapers. This would include any and all magnets as well. If you are 50k deep into this, spend the time to check every last piece of metal.
Have you checked for stray voltage?
Personally I would take everything off line for some time. Keep your macro going. Remove all bio pellets, denitrator, ca reactor, etc. Try going simple with your approach. Get the term "ULNS" out of your head. If you can keep your n03 around 5ppm then do so. Your p04 may go up a bit if you take GFO/GAC offline, but your macro should soak up some or more of it.
I doubt seriously it's your lights. Corals can live, but not thrive in a huge variety of lighting. Many reefers keep all corals under LED's so we know it can be done.
Last thing I would check is your procedures of "dipping/acclimating" your corals. One thing you may want to try is finding a source for coral you trust 110% and not dip them. Slowly acclimate them to temp AND your water paramters....from what I gathered you are dipping, temp acclimating, and throwing them in your tank. I would highly advise against this.