This sounds like a major increase in bio load, which means the filters need/needed time to increase bio bacteria populations to process the ammonia and nitrite. I wish you would give actual numbers for both the ammonia and nitrite level, and feel it would be advantageous for you to have a KH test kit to monitor and report the KH level. I suspect the ammonia levels went very high initially, and may be coming down to a reasonable value, but it would definitely cause the fish to be stressed. After the ammonia is processed by the bio bacteria it becomes nitrites and nitrites will combine with the red blood cells and turn them into brown blood cells that cannot carry oxygen so the fish can suffocate in water with plenty of oxygen. Adding about 1 pound of salt per 100 gallons will give protection from the nitrites.
Zone 7 A/B
Keep your words sweet. You never know when you may have to eat them.
Richard