Dilution is the Solution to Pollution
I suspect you just had a perfect storm of things that by themselves would not have been a big deal. I think you are on the right track, with water changes and such.
Do get plants in even if you do not intend keeping them. Mosses are great, wisteria, stem plants, fast growing plants.
One of the things that sometimes happens and I think is likely in your case is a cascade, the plants and fish being obvious, but if a die-off in the microorganisms, as well as worms and fungus and all the little creatures that make the plants possible die that can also foul the water, I suspect that when you vacuumed the gravel this is what you kicked up. At the same time getting oxygen and things moving is (or was) part of the cure.
One of the problems with our ammonia tests are that the ďammonia eventĒ is often over so fast, we do not see it at all. Sudden increases in Nitrates that cannot be explained by dosing are usually our best evidence.
The other is taking a close look at the dead critters, I know this grosses a lot of folks out, but even observations about streaking on the body, what the poop is like, a look inside the gills. The blood is often a very obvious clue, provide answers.
Keep dosing nutrients, I know it seems strange but the stuff in the water from salts you dose are rarely a problem.
I think things will get back to normal pretty quickly, though you will not be as likely to take it for granted. My only real advice is any time you see anything that looks like a filter problem, especially when keeping messy carnivores, is water change.