Dr Ron always said that the pyramids eat what they rest on. He said that the ones that eat snails don't eat clams and visa versa.
In one of my tanks, I have the snail eating ones. They came from a cup of sand from another reefer. In that tank I also have a 6" plus maxima clam and they have never bothered it.
For the snail ones, they like my Trochus the best. I used to regularly pull the Trochus out and carefully wipe off the pyramid snails off with my finger or a toothpick. Then, I would put the Trochus back. Now, I hardly ever see the pyramid snails.
Now that you know where the pyramids like to hang out on your clam, I would pull the clam out every 2 to 3 days and check it for the pyramids. Before long, the population of them should drop and hopefully your clam will regain enough strength to make a full recovery.
If your clam eventually dies (and assuming your pyramids don't eat snails), you should be able to get rid of the pyramids by leaving clams out of your tank for a few months. Per Dr Ron, since they won't have a host to feed on, they will die.
Best of luck,
Roy