Brown spots on Goldfish-not ammonia

Question
The tank has been set up for a couple of months.  There was some bouncing around of chemicals, but water changes and additives were attended to every day.
55 gal.
Two goldies, a 4" comet and 1" Shuby.
Undergravel filter plus TWO whisper 40 filters.
ph-7.8 -8
ammonia- 0-.25
nitrite- 0-.5
I have had to make water changes due to cycling.
I was doing 20-25% most every day because I had to keep the nitrites and ammonia in check.

First of all the 1" Shubunkin is perfectly fine.  The larger Comet is having problems.  A third fish was struck by tail rot and fungus, removed to hospital tank, but ultimately didn't make it.

4" goldfish had a white bump on his lip that turned into a cut. Then a scratch on the head appeared and a couple roughed up fins.

The scratch on the head turned blackish looking and has stayed that way for 5 days.  

In addition, each side has 2-3 scales missing.

Now the fish has brown areas, one on the tail, a few on one side of him, while the other side is fine.  Besides the one on the tail, they seem somewhat scale specific, like a 'brown scale' more than a big spot covering many scales.

Been treating 8 days Melafix. 4 tablesppons salt in 55 gal, water changes to keep chemicals correct.

I decided, since the only other fish is 1 " long and cant be bullying, that a decoration was beating up the fish.

I removed the decoration a couple days ago and there were several 2-3" long whispy white cottony clouds floating around.  Big grayish white clouds.

I had huge amounts of what seem to be fungus on the decoration.  None really on the fish, but I started Pimafix which supposedly addresses fungus.

The fish is continueing to get brown areas on one side.  I have researched forever and see "too many fish in the tank, over-feeding, and high ammonia", but this is not the case.  Ammonia has always been monitored and has been free ammonia-0 at all times and now total ammonia-0.

The fish swims around, eats gravel, and acts perfectly normal, but the blackish spots are growing.

Is it bacteria that Melafix didn't fix?  Is it some parasite that prefers one side of the fish?  I am stumped.

I don't want to dump every med in the book in the tank, but was considering PraziPro to clear out any parasites.  I actually saw a recommendation to use PraziPro once a year as a precaution, so figured it probably woudldn't hurt.

Please help me before my Gold fish turns into a spotted leopard fish.

Thanks!

Answer
Hi David;

"Melanophore migration" is common in goldfish that are in new tanks. Even after controlling most of the toxins the fish can still react to low concentrations of it that way. It can also be caused by scraping injuries. It's actually a good sign when they start to show dark scales because it means it is healing and whatever caused it is now gone. The blackish scales are kind of like "scabs". Just keep the tank clean like you already are and he will hopefully turn back to his normal coloration again in a few weeks once it fully heals and the damaged scales are replaced by new growth.

At Your Service;
Chris Robbins