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Strange symptoms leading to death of Tilapia breeding colony

Hi I need some help!!

I received my first shipment of Nile and Wami Tilapia on Wednesday. When we received them the wami male was dying and died about 30 mins later. The 5 niles females were living but two were extremely beat up. We separated the injured ones and salted the tank (the tank is a 55 gallon so 55 tablespoons of non iodized salt was added). We had a clay pot and pvc pipes in the tank (all boiled prior to adding).

Tank size 55 gallons
We cycled the tank for a month using goldfish (never had any deaths)
pH: 7.6-7.8
Ammonia: 0 ppm
Nitrites: 0
Nitrate: 20-40 ppm
We are on a well that has never been chlorinated 
Temp: 84-88
Bio-Wheel filter and water stones

These parameters held close to these number over the course of there life (1 week). The ammonia and nitrites never changed from 0. We tested everyday if not twice a day. Other than the salt treatment nothing else was added.

We fed them AquaNourish stage one (about 1/2 teaspoon through out a day). We bought this online and are trusting it is the correct feed. There is no label smells very fresh.

The fish started acting normal after 2 days even the beat up ones. 

A week and a day later from their arrival, Friday night they were eating well and happy (or so we thought).. Saturday morning we found the first dead fish (one of the ones that came beat up). We did about a 50% water change and salted again (half the amount this time). All the other females stopped eating. The next fish died that evening (the other beat up one). Their color was very pale, not eating, breathing heavy, bouncing off the bottom (almost in pattern with breathing, a hiccup almost). They stopped pooping and if they did it was almost a whitish color. The next morning, Sunday, we lost another fish and again that night. The last fish held on till Tuesday morning.

The next morning, Wednesday, our replacement wami male came in. He was in a totally different tank than the others and was cycled with ammonia 2weeks and then goldfish for a week. 

Parameters: Same as above only difference was the Nitrites were up a little to 0.25 ppm but came down within 12 hours back to 0.

When he arrived he had a batch of white fleshyness under his gills so we salted his 55 gallon tank (only holding 43 gallons of water so we added 43 tablespoons of salt). He seemed great, was eating and very active. Until last night, he was fine at 3 and at 6 is when he started breathing heavy, stopped eating, eyes bulging slightly, turned very pale. In the time we had him I never saw him poop . We had a hospital tank set up (29 gallon tank with nothing in it, had been salted to the exact amount of water). We moved him over, his color came back and was active again. We watched him until 12pm. This morning at 5:30 he was dead. 

We have raised fish before and never been at a loss like this!! I have searched and searched but nothing seems to have all the symptoms that we do. We want to know if we are missing something so please help!!

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Please just help us troubleshoot! Is there something we are missing?

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