Ok. so he is fine now and I solved my own problem. He just needed good water!
For whatever reason, my tank is cycling again. I can't believe that adding one fish (the puffer) to a 50g tank would have that effect, but I did clean the filter at the same time. Newbie mistake, I guess.
I changed 25% of my water becuase my levels were high: Ammonia - 1.0, Nitrite - 1.0, Nitrate - 20. I also upped the salt a bit on this change and will do so again tomorrow when I change a smaller % of water.
I am still going to leave him in the bucket for tonight with the air stone and a heater. He might get bored, but he is swimming around just fine.
I still welcome any advice on puffers or anything else in my tank.
Thanks,
John