All the fish in my tank are dying, why?

I have a 60 gallon saltwater tank that I set up about 3 months ago. I started off with Damsels, and gradually added other species until I had an nice colorful mix once the tank was well established and had cycled properly. We lost 2 damsels and a tomato clown in 2 weeks, then things went well for about 3 weeks. Everybody was happy and friendly, including the damsels (3 small) tomato clowns (2 small), horseshoe crabs (3) small dog-face puffer, yellow tang, fire fish (2) and one peppermint shrimp. Now they are dying at an alarming rate. We did get a reddish colored algae of some sort showing up on the glass, and I treated for it. The instructions said to remove my carbon filters and turn off my protein skimmer, so I did. Even with the treatment and limiting filtration, i am still losing fish. The only thing that is different as far as I can figure out is that I bought my saltwater from the fish store rather than making my own using instant ocean. We are running a 350 and 200 bio-wheels (carbon filters changed every 2 weeks), and a good quality protein skimmer. Any guesses or suggestions? I have tested and the ammonia, nitrate, nitrite, and ph are all reading really excellent (the best readings I have gotten since I set up the tanks with colors exactly matching the comparison cards). Please help? I only have my puffer, 2 damsels, 2 horseshoe crabs and my peppermint shrimp left and they are starting to look poorly!