The first one is probably a M. setosa (nice find!). The palys look like organisms to me. I'm not sure about the last one. Wait until it grows out more then ask again.
I don't quite understand. What are you hoping the dead clams are going to do for you and do you really think your LFS would want to buy dead clams off you?
It looks fine to me. There's a little vermetid snail on the left side in the second pic slightly blocking the mantle, but you can easily break that tube off.
There's no such thing as a truely bioluminescent coral. There's corals that'll look like it under actinics, but they're not bioluminescent. If that's what you're after, then look for green, yellow, orange, and red corals.
Those are either small polyps or big hermits. :) I also compared them to the size of the mysids. If the polyps are larger than I think, then it's probably an acan lord.
All tridcanca clams do. It's actually the zooxanthellae within the clams' mantle that feed off the nitrates though, but unless you have many clams it's not an effective way to export lots of nitrates.