I would say get as much aeration as possible going. Its possible the treatment damaged the gills. If you don't know what the actual problem is, you can't treat it! Have you treated your water changes for chlorine and chloramine? If shutting down the pump made things worse, get it running again.
I am so sorry about your fish losses. I know how difficult it can be. I haven't read everything posted in detail, but be sparing of feeding the fish until things settle down, and definitely keep those pumps and aerators going. And deep breathing exercises (for you). You obviously care about your fishes' good health and sometimes, everything we can do isn't enough.
I found my black one and he clearly had fin rot on tail. Barely alive so instead of him suffering I put him down with clove oil. I made the disision to remove my 3 older with and put in hospital tank and started giving them erythromycin. I also notice my orange one seems to have a grayish film . after reading this I decided to try the antibiotic.
Bacterial Gill Disease
Fish will scratch against objects and appear listless. A grayish film may form on the body. Rapid breathing in fish may be accompanied by gasping at the surface of the water, or the fish sitting on the bottom of the aquarium. Gills undergo severe damage,
I figured at this rate is loose them anyways doing nothing so nothing to loose.
Ok I just noticed one of my fish keeps flashing to rub on bottom or container like he is trying to scratch his side. Iv tryed looking for ich but he is mostly white but after my black one died I looked at him good and could almost swear he had salt looking specks but there weren't a lot so I could not be sure. I remember having a fish with it years ago in aquarium and it was really obvious this not so much. But know with this fish scraping bottom should I start treating for ich or wait. Problem is the fish I have left except one orange have a lot if white on them.I have api ich cure so should I treat them? I don't see anything on orange but could he have had them and they fell off . he is just sitting on bottom.
Update: I hope I'm on the right track, right now they are being treated with api fin and body cure Doxycycline in a Rubbermaid hospital container. I think I already mentioned that I started with erythromycin but switched to Doxycycline. It is the second day on this and after moving all the bubbles on suface I could see my orange one that was just sitting on bottom now swimming around. As far as the other 5 I can see 4 swimming and the white one is very hard to see because the water is so clouded from medicine. The cloudyness has me worried because if there is as an ich outbreak I would never know it.
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