It appears that you may have several unrelated problems that are inhibiting your success. Hopefully these suggestions will be of some assistance.
You didn't give a lot of details with regard to your fragmenting methodology, but I may have missed it in this epic thread. Do you use oxidizing gents or antibiotics after taking cuttings? Do you segregate damaged/diseased corals and sterilize & sharpen your instruments? A stock solution of potassium permanganate can be used for swabbing infected areas, dips, sterilizing instruments, increasing dissolved oxygen & redox, and neutralizing chemicals & medications in your tanks (turning your hands brown is fun too).
Losing an entire tank of ricordia sounds more like a bacterial infection, than a water quality or lighting issue. I find chloramphenical and neomycin (in concert) to be a good catch-all regimen. Give infected corals a one hour bath in 250Mg/gallon (of each) for one hour. This elevated dose will kill a broad spectrum of bacteria and fungus without jeopardizing water quality in the holding tanks. Chloramphenical can be hard to track down in some states, but neomycin is cheap and readily available at a farm co-op store. It's used for pigs and turkeys.
While I'm against the over-use of antibiotics in human and animal use, corals are a different story. You are fighting bacteria and pathogens that are from the ocean and (hopefully) have never been exposed to antibiotics, and subsequently have no resistance. In the long run you may have to rotate the type of antibiotics you use to avoid resistant strains within your facility. Furan based drugs like furanace, nitrofurazone and (my favourite) nifurpirinol will come in handy in that event. Make sure you aren't using oxidizing agents at the same time as the antibiotics (I know...you're an RN, but I'm assuming nothing).
Another good practice for disease control, water quality & clarity is ozonation. Overkill is not an issue as you're dosing plankton from culture vessels on a regular basis, thus replacing anything that may get zapped. An ozonizer could be used for a few hours daily. It could be plumbed into your blower effluent so it would supply all of your airlines. It could be set-up on a timer to avoid overkill and residual ozone. I would install a sniffer (detector) for your own safety. Using it at night would also avoid exposure and raise nighttime PH.
You mentioned "cutting a sarcophyton in half" in one of your posts. This is an overly invasive cloning method. It will yield large clones, but the mother colony will require too much downtime to heal. You may also consider keeping healthy mother colonies in one tank and freshly cut mothers in a convalescent tank. This will limit stress and water quality issues that will inhibit the growth and health of the whole colony.
The true issue I see here is a lack of pro-biotics, rather than antibiotics. You're holding tanks appear to be very clinical. I don't see much of a substrate, live rock, algae or critters growing on your eggcrate. Corals never thrive in such conditions. I've visited many hobbyist reef tanks and have noticed that coral growth is always better in their display tank than it is in their culture tanks.
I see your method to be parallel to hydroponic plant growers. You're trying to harness nature and provide only the necessities (calcium, magnesium, carbonates, sunlight, zooplankton, phytoplankton etc.). This method works for hydroponic growers as they only raise their stock for a matter of months, not years. They can push the margin, knowing that it's a finite growth period. Corals on the other hand will experience growing pains.
A higher order ecosystem is the key to success. You've strayed too far from natures recipe, and need to reframe your approach. You can achieve this by adding a reverse photoperiod refugium to each tank. Place a shallow rubbermaid container under your stands and illuminate them at night with economical daylight twist bulbs. Shield the containers from daylight. You can run these refugia on a modest powerhead return and standpipe. You may even be able to power them with a solar battery system, as the prices and quality of these units are getting better all the time. The standpipe will aid in gas exchange as an added bonus. A reverse photoperiod will eliminate the coral bleaching PH shifts you likely have at night.
In addition to regulating gas exchange, macro algae will foster the growth of zooplankton, export nutrients, has antibacterial properties, and can be harvested and sold. Gracilaria and chaetomorpha are efficient, stable and marketable varieties to work with. Macro algae culture will also supply Co2 during the day for symbiotic zooxanthellae, eliminating your need for fish in the system. While fish can add nutrients to your tanks, these are phosphate, nitrate, and silicates than can be supplied through phytoplankton and zooplankton feeding.
Gas exchange may or may not be an issue. It's hard to judge your flow dynamics as the airlifts are shut off in the pictures. The addition of a standpipe drain for the refugium will remove surfactants and help with gas exchange nonetheless.
How much substrate, if any, do you have? This is another key part of the equation for filtration, buffering, and fostering greater biodiversity (zooplankton & water polishing benthic invertebrates such as sponges, worms, and tunicates).
You're missing the boat on passive live rock mariculture. You've got more than enough room in those tanks for live rock. Live rock will stabilize nitrification and denitrification, with a marketable residual. Use 50% colonized rock with 50% new rock. Harvest the older half every six to nine months (FIFO), once it is covered in coraline algae and stray polyps.
Your tanks don't appear to have any of the typical signs of healthy conditions such as coraline growth and benthic invertebrates. If I followed your post correctly, you've only been running for 14 months. That's not enough time to stabilize a relatively bare tank that has had little inoculation, and likely no chemical assistance with "cycling" (i.e.. ammonium chloride & sodium nitrate). I find that fully equipped and stocked reef tanks take at least six to nine months before coral growth is significant and benthic invertebrates populate the undersides of corals and eggcrate. Do you have a large population of serpulid worms in your substrate yet? You may be trying to run before you can walk. I know 4 1/2 years is a long time for this project, but it takes as long as it takes when you're establishing your tanks.
When corals are kept in an incomplete ecosystem with an insufficient supply of phyto and zooplankton, they must rely on symbiotic algae for nutrients (carbohydrates). This steady diet of sugars is taxing on their health and colours are diminished. Many greenhouse corals have a brown layer of zooxanthellae that obscures the fluorescent UV blocking pigments below. Once your corals are moved to a hobbyist tank with less light and more plankton, the brown colour dissipates, revealing the intense underlying colours (as you reported in one of your posts).
Rather than spending your resources on water changes, you should focus your efforts on nitrate & phosphate reducing organisms, nutrient export and exchange resins. You could use barrels buried beneath your greenhouse for bulk denitrification and buffering. Water changes are not cost effective as they and are limited to temporary reduction of excess nutrients, in only a small percentage of the water volume. i.e.. a 20 % water change will reduce organics by 20%.
Recent studies, tracking the quality of salt mixes and content of existing aquarium water, have proven that you may be adding more heavy metals than what is found in natural sea water. Nutrient import brings with it many trace elements (heavy metals). Water changes may add further to this problem.
http://reefkeeping.com/issues/2002-12/rs/feature/index.php
You may also benefit from the use of coral cleaning symbients, such as shrimp, starfish, crabs and fish. Many fish and invertebrates consume dead coral tissue. Tangs and even butterflies can be moved from tank to tank to remove sloughing tissue, fungus and necrosis.
Your protein skimmers may also need some upgrading to help with nutrient export. Commercial mariculture requires significant nutrient import and subsequent export. I assume you have culture containers for phytoplankton, copepods, mysid shrimp, anthropods, and brine shrimp? You may be able to set-up a system whereby nutrient rich water can be dosed into the tank and exchanged with "clean" water for the majority of the day. This practice would yield maximum exposure to foodstuffs during feeding hours (perhaps at night) while maintaining water quality. You could use an ebb & flow system incorporating barrels buried below the tanks.
What kind of a buffering system are you using? You may have ion antagonism if you are using an imbalanced chemical regimen. The practice of dosing calcium hydroxide without balancing magnesium and carbonates will introduce free radicals that will wreak havoc on water chemistry and coral health. Calcium carbonate, gluconate, or chloride can be used in conjunction with calcium hydroxide in order to balance leftover negative ions (anions). Ion exchange resins like Chemipure will help, but they aren't viable in commercial mariculture applications. Sponsorship and endorsements go a long way. Try to build symbiotic relationships with manufacturers and distributors.
You must have an incredible amount of evaporation each day. Did you have 0 TDS during the de-ionizer incident? Even a minute amount of minerals in your source water would have a great effect on coral health if you have significant evaporation. I don't know what kind top-off system you use, but DI water will quickly leach VOC's from plastics and draw gasses out of the air.
If you were to use aragonite (calcium carbonate), dolomite (calcium magnesium carbonate, and celestite (strontium sulphate) in your source water reservoir, you would be able to stabilize the ion-hungry water and remineralize it at the same time. The leftover sulphate anions (from the celestite) would be utilized as a nutrient source by denitrifying bacteria. A freshwater-style Co2 reactor could be used to lower the PH in the reservoir to aid in dissolution of the media. A second reservoir with an airlift and media should be used to buffer the PH and aerate the remineralized water. A holding tank with significant evaporation will stay cool, and receive enough remineralized top-up water to exclude the use of traditional calcium reactors and chemical dosing. Such a system is ionically balanced, addresses the chief deficits (calcium, carbonates, magnesium, strontium, and sulphur), and is cheap & easy to run.
). Does it seem to have been a gradual thing i.e, maybe the waning light of winter. The only other thing that comes to mind is that maybe something with the water purification is leaching in at a small rate and building up. 
). He also realizes that as the sun gets lower in the sky, i start removing much of the shade for the tanks and the shade over the gh itself. He said he would like to see the UV cut-off around 390 nm instead of the 360 nm that I have, but he didn't think that would cause the results i am seeing. That was when I tried the acrylic panels over a few of the tanks like Actinodiscus, Anthelia, Star polyps.
