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I just finished reading your entire thread. First, let me say I'm sorry for your losses. 2nd thing I'd like to say is that I don't believe you're dealing with simply an internal parasite problem.
As one other member mentioned, the effects of high nitrates likely played a huge role in your issues, but I also see a number of other issues that stand out.
Lets address the "ruffled scales". In this description I am wondering if by ruffled, you mean that the scales have lifted, almost a pine cone type of effect? If that is the case, I would have to assume you are dealing with dropsy. That is one of the most common symptoms of that particular disease, and unfortunately, there is no cure. Any fish suffering with dropsy should be moved to a quarantine tank to avoid the risk of any other fish eating the infected fish's organs if/when it dies. That is how dropsy is passed from one fish to the next.
Another thing I'd like to address is the large water changes. Chlorine poisoning isn't the only thing that happens with large water changes, although yes, that is, too, a concern. Large water changes rapidly change water chemistry, which can cause pH shock, and just shock in general to the organs of the fish. This can cause instant death, such as you saw with the mass die off after a larger change, but it can also cause internal damage that doesn't always kill immediately. This damage, such as organs that no longer function normally, can lead to a slow and gradual death, usually brought on by gradual organ failure or the inability of damaged organs to do what they are supposed to... such as filtering blood, digesting food, providing oxygen, etc. High nitrates for a long period of time will also cause organ damage.
It sounds to me like you are dealing with a large combination of issues, and if you wish for help in sorting it out one thing at a time and treating it properly/safely, I am more than happy to do that with you, but I prefer to start over from your original thread... here... 1 question and answer at a time to sort it out. Because this has been going on for so long I will need to map this on paper here so I can avoid confusion.
In answer to your question about the change in color/vibrance of the scales... there are a few things that can cause that. Old age is usually the most common cause, but organ damage can also cause it, as can nutrition issues and water quality issues.
One thing I noticed through your entire account is that you never appeared to have tested the water? You never listed any params for water other than nitrates at 0 in some of the tanks. 0 nitrates in an established tank with fish and food going in, that alone indicates a problem with the biological cycle in the tank, and should be dealt with as a separate entity because it will affect not only the overall health of the fish, but also their responses to medications/treatments and long term recovery, immune system, and behavior, such as not eating. When there are fish and food in a tank and nitrates are at 0, then ammonia and nitrite become a concern, and should also be monitored closely. Long term high nitrate issues will also cause pH to drop, sometimes very rapidly... and large water changes will help to fix this, but can shock the fish's systems if the change is too drastic too fast.
I would very much like to help you if that is ok? The first step for that would be to map out each tank one at a time, tank size, each tanks population (what species and how many of each), water params for ammonia, nitrite, nitrate, and pH, water temp, type of filtration, and a list of anything going into the tank such as food, meds, clean water (how much and how often), etc.
One note for you before I finish this post... large water changes are dangerous, even when the problem is bad. Small and frequent, such as 10 - 15% each day is much safer (and more effective) than 50% once/wk. Especially when dealing with nitrate issues, which happen gradually over a long period of time. Just as the fish are usually able to adapt to the changes in the wrong direction if the changes are slow, so they can adapt to the changes in the right direction, but again, they must be slow to avoid shock to the fish's organs.
I hope this has helped. I look forward to helping you resolve the issues you are still facing so you don't need to suffer any further losses.