He could be settling in, Sg might be off or Sg change from the store to your tank might have shocked him
There are many different things that could cause a color change to the darker shades. Normally parasites would be indicated by stringy poop and sunken bellys thats seem to stay that way even after feeding.
How old is the tank, how big is the tank and what are parameters if you dont mind me asking , it will be alot easier to pin point the problem
You said he had poop on his belly and that was making it completely black??
Oh and i would be very careful netting Puffers in general as this may stress them enough to make them puff and if they do so out of water they can injest air which they have alot of trouble expelling were as water can be expelled without a problem
