This is going to be a fairly long post. So I recently did made a silly mistake to a tank that has been running since 2012: I did a large water change then threw out both filters out the same time. I have a 55 gallon tank with a male jack dempsey, female jack demspey, and convict. These fish have grown up together since I first set the tank up in 2012 and all get along great for the most part. Recently, I began to notice my male JD "jack" was not being himself. He was hiding a lot and breathing very heavy. I will be the first to admit that over the last year or so I have not taken the best care of the tank. I always fed the fish but was not consistent with the water changes like I should be. I also noticed a large split in the crevice between his caudal fin and dorsal fin, a very painful looking split at that. I did a large water change, removed the activated carbon, and dosed the tank with melafix. I was medicating the tank for about a week or so. Shortly after I noticed what appeared to be a fungus on his body, he was still breathing heavy. I did another water change and then dosed the tank with PraziPro as I was wondering if the heavy breathing was due to gill flukes and poor water parameters. Another 2 weeks went by. His breathing seems a lot more normal now. However, he is still sitting on the bottom of the tank. He gets very excited when I get the food out but right after eating he returns to the bottom. I have been watching the tank like a mother hen the last few weeks since I threw out the filter cartridges that contained my biocyle (idiot).
My tank readings today are as follows:
Ammonia: 0.5 ppm
Nitrite: 0 ppm
Nitrate: 0 ppm
pH: 6.8
My nitrates were at 5.0 ppm yesterday before I did a 5 gallon water change. Today they are down to 0 ppm. I have been doing daily water changes of about 5-10 gallons to try and knock the ammonia levels down. The last few days they have been staying at 0.5 ppm. Is my cycle almost back? since my levels rose then came back to 0 ppm? Is it okay to do daily water changes of 5 gallons or so or is this causing too much stress to the fish? "Jack" is also very dark. He is a beautiful fish but he has compeltely lost of his his bright sparkles and is very dark. Where should I go from here? I am worried I'm going to lose him

What do you guys think? Sorry for the novel.