Well, after a rough couple of weeks with my fish problems I think that my problems are solved *knock on wood*. I did a 100% water change today - that's right 100%. It was a pain, but worth it. It is now about 8 hours after it's complete and everything seems to be fine. I got some sps frags from a friend yesterday and I'm getting full polyp extension and all the other corals that I acquired from friends are doing well - GSP's, leathers, xenia. The fish that's in my frag system (now hooked up with the main system) is doing well. Ate well after the water change and wasn't shy. I got another 100 lbs of rock yesterday that's well seasoned so there shouldn't be much of a spike, if any. Here's a picture of the tank almost drained.
It was a chore, but all worth it in the end. I will attribute my problems to either a bad batch of salt or something that leached in unknowingly. I am praying that this does the trick as I was ready to throw the towel in.