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I use two Mag 9.5's for my system, and calculate after head loss, that I'm getting about 1500 GPH through the two overflow bulkheads. Eheim 1262's would be a good consideration too. Since you have to heat the water anyway, the only time heat would be a consideration would be if you had to start...
What were you feeding it? Smaller clams usually need a supplement of a good Phyto product. Here's a little reading:
http://www.wetwebmedia.com/ca/volume_4/V4I3/Tridacna/artGotTridacna.htm
Any of your fish nipping at its mantle? Any possibility of Pyramid Snails...
I use almost all of the water I've made for WC's, about 25 gal. every two weeks. As soon as I've used it I make more, and keep it aerated, heated and mixed until the next WC. Here's a good article:
http://successfulreefkeeping.com/learn/salinity-mixing-saltwater/