Tom,
I don't think that your problems are related to iron or Mn sequestering by the clams. Your nitrates may be the problem as you have indicated. If you are doing regular water changes with a brand salt, there should be enough iron and Mn available.

I have supplemented with iron & Mn on and off through the years and have not noticed much difference in the corals or livestock, with the exception of the macro algae. I started supplementing when I could not get good macro algae growth and that solved my problem.