I've not done what you are doing...but I think you realize that Ammonia is far more likely to kill your fish than whatever it is that you are trying to treat. Water changes are the only way that you are going to keep that Ammonia level low in the short term.
You could transfer in a piece of rock from your system, but you may not want that rock back again after you've medicated it.
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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