The LFS says I actually have a small ammonia rise. They said it was about 0.5. So, I got some ammonia treatment, and that seems to have cleared the water a little. She said that the ammonia was directly related to the bacteria bloom which is making the water cloudy. She said that was also related to the puffer looking upset. Just for FYI she said that it was not ich due to the fact it is not raised off the skin like salt crystals, it is just skin discoloration.
So, that's all good news, and I sure hope the water starts to clear soon. I also added Lee's protein skimmer today too.
(Keeping fingers crossed)

Thanks for all the help and great information!