Matt, I could be way off, but I dont think that clam looks too bad...and what do you mean by incurrent siphon? But I think the Calcium is low, I dont see any white growth on that shell from the first pic.
But to answer your question....Oceans is correct I think. That looks exactly like the little pineapple lookin tunicates that I have everywhere in my tank.. Would give you a picture if I had a digital camera. Anyways, I dont have the first freakin clue what is on stuck on him on the left side of that pic, looks like a tubey worm, but can't be for sure. Regardless, I've never known any parasites on clams other than those little white rice lookin buggers that get attached to the shell. I know this aint exactly techinical terms, but you get the drift.