Mainly at this point I am thinking some toxin got into the tank, and a large water change would remove all of it. I look at it this way: a large water change is no different than when you bring a new coral home... either one is a 100% water change from the coral's point of view. I made sure alk, SG, Ca, and temp were relatively close as well. That said, maybe I wont do a 100% change on the main tank after my experience with the frag tank. A few 50% changes over a few weeks should get me close enough.
Today I took the rest of the system apart. Rinsed the sump out and put it back, inspected all pumps, reactors, skimmer, etc. As of now the main tank is running with two tunzes for circulation and LR for filtration. All fish, crabs, snails, urchins, cuke, clam, zoas etc are doing fine.
Wentreefgirl, thanks for the offer and I will definantly hit you up on it. I'm looking to go a little hardier and simpler this time around, and caps would be perfect.