Thanks guys.
He spent a couple of days soaking before his eyes clouded over. He sometimes does this so not a huge deal. He has no mites. No parasites. I always check for that, for anything in his water. He's clean.
When he got sick, I cleaned his terrarium about every 3 days. Lined it with paper towels and removed all the ornaments. I replaced his hide with a cereal box, which I also replaced weekly.
I don't know what he had. The enamel from his scales peeled off. I searched online and only found one other report of this. The guy said his vet didn't know what it was and pumped him full of antibiotics. I didn't want to do that. To this day, I don't know if he had scale rot or something else.
I applied triple action poly to the bad areas and kept a close eye. He ate fine. He shed three weeks later and that went fine.
He ate again, but I noticed he defecated rather quickly, twice in one day. I've never seen that before. The last movement he had looked awful watery, like it was covered in slime... really mucousy. The uric acid was also really yellow.
I don't know if he's still sick as I never really played close attention to his crap before. I also probably wouldn't notice these subtleties as he was on shavings before, and no paper towels. So I don't know if he's sick or not. I go by his activity and his hunger. He's curious, moves around fine, and feeds like normal.
Anyway, he's almost 3 years old so I don't know if 3 weeks and 3 mice are enough to make him grow THAT much so I don't feel this shed is indicative of growth. I keep a close eye and will keep him in his "hospital" habitat for a while longer...
At least one good thing came from all this. I really bonded with him during all this