First of all I'd like to say, thank you all for so much valuable information. I'm a longtime forum lurker, and this may actually be my first post. I've been doing a lot of reading in the Fish Problems section, but I still don't have the answer, or I may be dense

I should probably start with system specifics.
My wife and I are new to aquaponics, and in fact, I am new to gardening. I am not much interested in farming, but I am very interested in eating, and we are trying to work toward a position where we can grow most of our vegetables and then some. We became interested in developing our own aquaponics system, and we attended a couple of Rob's workshops. After that, we were so stirred up, we immediately started researching what to do next. I'm not gonna bore you all with the gory details. Basically, we cleared a spot, built a fairly large hoop house, built a fairly large system, cycled w/o fish, added fish and planted plant starts, and happily watched as the plants and fish grew up together. My wife teaches at the high school, and I wanted to have the thing built and cycled and ready by the time school ended for the summer so I could just hand it over to her and she could do the "easy" part. Turns out building it WAS the easy part.
Here's what we've got:26' X 48' hoop house near Bastrop Texas
800 gallon fish tank sunk into the ground, (attempt to regulate water temps). Much aeration from blower pump.
Five 5' X 10' growbeds expanded shale media, flood and drain on timer and indexing valve
Growbeds drain to a raft, 4' X 32' X 12" deep. Raft has much much aeration from blower pump.
Raft drains back to the fish tank.
We are rainwater collection exclusively, so water in system never had any chemicals to speak of.
We've always had a film cover on the greenhouse, insect netting walls so creatures can't come in nor can rain.
We got all the plumbing working just find finally, used clear ammonia to invite the bacteria, boosting with bacteria in a bottle, I don't remember the brand. Then added 100 channel catfish fingerlings from Overton's hatchery. We decided on channel cats after hearing that they are more tolerant of winter cooler water temps. We’ve been feeding them Cargill Aquafeed floating food. All was good. We maybe lost one or two fish to unknown causes at first, but they fed well from the beginning. We started out feeding them all they wanted, twice a day. We would slow down so no food remained.
Levels:PH has always been on the low end, (rainwater), and our media is inert.
Ammonia and Nitrites have always been 0 or close to it.
Nitrates have alway been very high. Dark red/brown test tube.
The problem:My wife thinks the problem started when she bought some plant starts and didn’t quarantine, or otherwise inspect for stowaways. We ended up with a major whitefly infestation, with aphids thrown in for good measure. She’d read that you can try diluted dishsoap solution spray, so she tried that a few times. It seemed to make the catfish act stupid, so we stopped using the soap. We performed a 1/3rd water change about once a week, and the fish seemed to get better, but not for long.
A fellow aquapon suggested that the only way he’d ever found to rid your system of the whiteflies, is to rip out all plants, wait two weeks and start over. Disheartening. So that’s what we did. We figured that if a very experienced farmer couldn’t solve the whitefly problem without taking drastic measures, we didn’t really have a choice.
So that’s where we are now. New plants are growing, all started from seeds. Raft is full of romaine, grow beds have new kale, peas, collards, snow peas, other stuff. But they are a long way from having mature root system. I’ve always thought that without mature plants to filter the water, the high nitrate levels can’t be good for the fish. So, all this time, some to fish are still acting stupid, and what I mean is, they swim upside-down or on their sides, they swim straight for the side and run into it. Right now, there are one or two that are hanging there at the surface, nose up. Thay don’t appear to be gasping for air. When we would feed them, some would feed normally, while others would act like they wanted to feed, but not even open their mouth or even swim toward the floating food, as if they couldn’t see it. It was like they were trained to go to the surface to feed when food is present, but they weren’t hungry, or able. Some fish would lay on their sides on the bottom for weeks, still alive.
Eventually, I got rid of nine or ten fish as it looked like they weren’t gonna get better. Right now I’ve got ten fish in a quarantine tank. I bought Epsom Salts and want to try that to see if I can help them. We’re buying big bags of Morton’s Pool Salt today, and after reading a bunch this morning, am thinking of salting the whole system to 3ppt. 45 pounds salt to our 1800 gallons.
I’m thinking that maybe the fish became weakened from salt treatments, then the high nitrates finally got to them then perhaps that started succumbing to illness or parasite or something. One dead fish had very small lesions on one side.
I'm also wondering if I should look into somehow filtering the system water with some kind of in-line canister filter to try and control the nitrate level until our plants are up to the task. Is this a good idea?
I’m sorry I’ve been so long-winded and boring. What do ya’ll think? Is there help for us?