I basically did a 70% water change-I emptied out the entire tank (saving approx 2-3 gallons, after straining it) and rinsed/strained all the gravel at the bottom because there was so much gunk floating around when I stirred things up. Once I refilled the tank, I checked most of the params. and the ammonia levels were just above 0ppm and when I added this stuff that helps neutralize it, and rechecked the levels, it was 0ppm.
I also just double checked nitrite and ammonia, both are at 0ppm. He's still pretty sluggish, but is swimming around a little bit more.