His tail does seem to be a little bit less clamped than it was in the earlier photos. Hopefully that's a sign that the improved water conditions and the fake plants and things you've added are helping him feel a little better and less stressed, which is great. Means he stands a better chance of recovering and also a better chance of surviving any meds that might be needed. He's still a very poorly little fish though, and I'm less concerned about fin rot at this point, than I am about his long, skinny shape and general droopiness. If there is some fin rot, then keeping the water very clean is crucial, and you're already doing that.
I also only learned about keeping tanks bare bottom being stressful for fish the other day from here too; I kept mine bare bottom because of meds/cleaning etc, but it makes total sense that the lights and shadows on a bare bottom stresses them out. Makes me think of swimming out to sea, and reaching that point where the sandy bottom suddenly stops, and there's a deep drop off. You feel it in the pit of your stomach, that there could be anything down there beneath you... *shudder*. Will make sure I add a very thin layer of sand or gravel to mine in future too.
Bear in mind that this might be a pretty long process, and you might be quarantining and trying out treatments for a while. Also that these things take time, and rushing to throw more meds or treatments at it to try to make things better, faster, can kill your fish quicker than any disease. He came very close to dying, and right now, it's more like nursing him back to life after he had an almost fatal accident. It will take a while, and a lot of clean water, for his body to heal from that, and he may never look quite as normal as he likely did before that.
But there's also a very solid chance that he also has some parasite, worms, or other issue that will need to be treated, and that it's unconnected to the ammonia poisoning, but hard to pinpoint because of the near death poisoning experience. Constantly refreshed clean water is the most important factor in fish health, so for now, continue with the frequent water changes, feed good quality foods, make the quarantine tank as low stress as possible, as you have been doing, and see how he's doing after he's had some time. @Deanasue, @Colin_T and @Byron know a lot about fish health and diseases, and would have a much better idea of whether to move to another type of treatment and when to try that than I do, hopefully they can help?
Don't be tempted to decide that the healthy looking fish is okay, and move him from quarantine into your main tank. If there's a parasite or something in the sickly fish, the healthy looking fish likely has it too, and will spread it to your main tank. Make sure that they're both healthy and disease free before moving either of them into your main.
