you mentioned above that you lost 2 table acros and a lot of your macro algae in your refugium. After this event, did you do any water changes?
see, a common problem with macro algae, especially caulerpa, is when it dies, it releases all of the toxic compounds it has absorbed, back into your tank. This can be extremely deadly to your tank inhabitants.
this may be a reason that your clams are showing signs of stress. And losing to acros, im assuming RTN or possibly bleaching, also could mean that you have some water quality issues.
how often are you performing water changes? i would suggest with a bioload as heavy as yours, you should shoot for 10% a week, you have clams and corals that demand very pristine water conditions in order to do their very best.
i may have missed it, but i dont think you mentioned your maintenance schedule.
also, in response to your limit of DT's because of algae, i wouldnt limit the clams main food source, if you feed your tank, you may get an algae bloom, but after a while your tank will balance out as soon as it figures out how to handle the new increased amount of food.
this happened to me when i began feeding heavier, and now im fine. little algae growth.
but consider doing more frequent water changes, and try to keep freshwater dipping to a last resort i would say, because im sure that puts a great deal of stress on the animal.
HTH