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I'm sorry no one answered your post but I'll see if I can help here.
IAL doesn't stain tanks, it "stains" water but not the tanks.
You don't need to sterilize a tank after rot, it's carried on the fish not the ornaments or anything. The filter will be fine the way it is although depending on which antibiotics you use could have ruined your cycle if you had one going but otherwise you can just set it up and let it go. Without an ammonia source you may lose the cycle anyway since the bacteria will stall without a food source.
 
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