Well, I thought he was doing better but we lost him today. Poor little guy. He was starting to get really active again too and his bumps looked to be decreasing in size. I suppose whatever he had just had too strong of a foothold. None of the other fish are showing any symptoms at this time and it's been many days. Strange that two of them fell prey to the same mysterious illness right after the substrate change though they were housed in different containers during the task. Maybe it was something to do with the new substrate or more likely bullying from my GBR after everyone was put back in the tank. Guess I'll never know unless another fish comes down with it.
The good news is my ammonia levels are coming back down. That was probably caused by a combination of substrate change and melting anacharis and val. Neither of them did well after I planted them and I removed them last night to help reduce ammonia emissions. Put in some wisteria, Rotala and another large anubias. Still need more background plants that won't melt though.