I'd suggest using ONLY distilled/di water in your tank, not tap water - too many impurities in tap water.
In the other thread you mentioned your nitrate running about 20 -- big eating and big pooping by the puffer and his leftovers is going to crank that up and possibly even cause small ammonia spikes if uneaten bits are left on the bottom. This can aggrivate the problems you are having.
In the other thread I described how to wean a lionfish onto prepared foods, I have never met a puffer that wouldn't take prepared foods. Freshwater fishes are not a good foodstuff for saltwater fishes. They can be useful to initiate a feeding response if the animal is picky, but get them onto preparations that are for them as quickly as possible and avoid letting waste hit the bottome to rot.
San Francisco Bay Brand makes a nice plankton mix for puffers, they also love squid, clams, mussel, silversides, krill, shrimp and other goodies. These foods are more appropriate as they are saltwater creatures too.
Jenn
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LFS Owner:
Imagine Ocean
Just keep skimming, just keep skimming, just keep skimming, skimming skimming! What do we do? We skim, skim, skim!
I'd stick with prepared foods for now, high quality flake (Omega One or OSI brands are good) and perhaps some enriched Brine Shrimp or 
